Cannot update published website without errors: requires deletion of site, then creating a new one.

Question

Hello all,
This has been a long persisting issue since we purchased Muse in January 2013, but has since then led to a shutdown of my office's website and email in September. Multiple support technicians were eventually able to restore the website, as well as our email function, but the core of the problem lies in the fact that when I update my website, it becomes entirely scrambled, and the only solution provided to me right now is that I need to delete my site completely (through Adobe Business Catalyst) and then create a new one, while transferring over the same domain information. I have yet to receive guidance on how to resolve this issue properly:
September 06 Email: detailing the series of events
Good evening, Zak,
I am reluctant to bring this to your attention because of the comprehensive nature of the following, but I have been told that my absolute last effort should be to contact you with what has been a persistent problem since the last time we had mediated this particular issue. Essentially, when publishing a website multiple times, sooner than later the format becomes scrambled when viewed online. I am being told I am the only customer known to have this issue, and that it needs to be investigated deeper.
This is a blurb from our original conversation in March 2013:
(The whole thread may be found at the following address: http://forums.adobe.com/message/5653912#5653912)
9.Zak Williamson (Adobe), 
Mar 12, 2013 4:03 PM   in reply to essbarr
I'm also puzzled. This isn't a problem I've seen before for a site published to Business Catalyst.
Please try publishing again, this time to a new temporary site (they're free). You can choose this option under More Options in the Publish dialog. I'm curious whether publishing to a new empty trial site works.
If that doesn't work, please send me the .muse file at [email protected] along with a link to this thread. If the file is larger than 20Mb you can use a service like Adobe SendNow, SendThisFile, WeTransfer, Dropbox, etc.
Thanks.
10.essbarr, 
Mar 13, 2013 6:49 AM   in reply to Zak Williamson (Adobe)
Hi Zak,
I published the website to a new temporary site, and it worked beautifully. Now I just have to fuss with the horizontal bar, and then I'll be super happy. Thank you for your help!
Sincerely,
Sarah
Since this bit of advice, I have freely published to a new temporary site every time the website gets scrambled. I have had temporary websites titled:
argponline01.businesscatalyst.com
through
argponline15.businesscatalyst.com
along with a bunch more than I cannot recall.
and Muse files titled:
argp-uc.muse
argponline.muse
argponline_02.muse
through
argponline_05.muse
argponine_3A.muse
argponline_3B.muse
and currently, my file name is
argponline_4.muse (dropbox link)
I am using Muse on a Mac Powerbook, OSX 10.8.4.
I don't know how much of the above is relevant, but maybe it makes a difference to you.
The timestamp on the following thread says September 5th, 2013 4.50AM, but I really sent it the evening of September 4th, 2013. No difference anyhow:
http://forums.adobe.com/message/5653912#5653912
What was going on in detail:
1
I made a few changes to my argponline_4.muse file on September 4th, 2013.
The published website at that point was argponlined.businesscatalyst.com (D).
The domain name was argponline.com .
(D) was published probably about two months previous, maybe longer ago.
When publishing (D) on September 4th, 2013, the website appeared scrambled.
I tried to publish only modified files, as well as publish the entire site, as well as close programs, and restart the laptop.
I decided to follow the advice given previously, and I published and launched argponlinef.businesscatalyst.com (F).
2
At this point I have two bookmarked websites for Adobe Business Catalyst Admin Consoles.
For (D), the Admin Console address was argponlined.businesscatalyst.com/AdminConsole/#!/Admin/Websites.aspx 
For (F), the Admin Console address was argponlinef.businesscatalyst.com/AdminConsole/#!/Admin/Websites.aspx
I was able to sign into both.
When signed into the Admin Console for (F), I tried to Add a New Domain, but was told that I only had a plan for one hosted website through Adobe Business Catalyst, and that I would need to purchase a plan that offered more hosted websites.
I signed into the Admin Console for (D) and deleted the domain, but given the option to keep associated files just in case, I opted yes, to keep them.
When signed into the Admin Console for (F), I tried to Add a New Domain, but received the following error message:
Domain already exists. Please delete all records associated with this domain before re-adding it.
There was nothing visible though the Admin Console for (D) to delete the associated records, so I deleted site (D) in its entirety.
I continued to try to Add a New Domain for (F), but continued to receive the same error Domain already exists...
3
At this point (the morning of September 6th, 2013) we have the following set of parts:
The published and launched site is argponlinef.businesscatalyst.com (F). 
For (F), the Admin Console address is argponlinef.businesscatalyst.com/AdminConsole/#!/Admin/Websites.aspx
The website is now completely down, and I have disrupted email service for the office.
I chatted with Lokesh, who determined this was a technical issue, and I was forwarded to Anshul.
Anshul's assessment is as follows:
Anshul: I see the error, Sarah it seems there are some Domain traces left with the system , I tried to clear then out and I am getting errors as well. In this case , we might need to escalate the case to higher level to have deeper investigation related to this issue.
Anshul: Sarah, the issue is the domain not the site. It seems like there are some traces related this domain in the backend. This issue is more of related to BC and not Muse. I will have this issue escalated and checked with the team and request them to run internal queries to clear the traces and then you should be able to add the domain.
4
Soon after I received the following message from Matt Baracz:
Matt Baracz (Adobe Business Catalyst Support)
Sep 06 10:50 (EEST)
Thank you for contacting us.
I have escalated this issue to our engineering team and have requested them to clear any references to the domain argponline.com from our database. Once cleared, you will then be able to re-add the domain successfully to your site.
As soon as I receive a response from engineering confirming that this has been actioned, I will let you know directly via this support ticket.
Regards,
Matt.
Around 3 or 4pm, I had not heard anything back, so I attempted to Add a New Domain through the Admin Console for (F). (Turns out Matt works in Australia, and was unable to alert me due to the time zone difference. Understandable!)
This was done successfully, so the website began to work again, but the email was still down.
5
I began a chat again, this time with Srividya. I was transferred to technical support and began conversation with Sanjit. The length of our conversation was probably around 3 hours, and I am so grateful for the time he put in. What a great guy.
He stated that he had gone through the case details and that Engineering had fixed the issue. We spent some time coordinating the Site Domain information through the Admin Console for (F). Ultimately, email is still not working (settings were probably updated around 5pm), but I understand sometimes it takes a while. Just wanted to note, the last time I updated the email settings it worked within a couple minutes. Varying lengths of time are expected, but I am still curious what effects those variations. Regardless.
6
The current situation is this:
My boss is a bit steamed that our website was down for a day and a half, and that our email is down for a relatively indeterminate amount of time. It's bad for business, and ultimately, I am responsible for these disruptions. I am incredibly concerned that the next time I update our website there will be a slew of problems, which have the potential to knock down service for the website and email again. I am desperate for a surefire way to simply and fluidly update our Adobe Muse website to Adobe Business Catalyst without making the same mistakes again.
I don't believe I did this the right way. I looked at FAQs, Community Forums, goDaddy Support and anything I could lay my eyes on to try to do things properly, but managed to make a few well-intentioned blunders. I continued to try undo the damage I've done in the past couple days, and with utter frustration, have not been able to fix them on my own. The people who have helped me thus far have done an amazing job, but ultimately, I am happier when I am not taking up their time, or panicking here.
When I first launched the website a few months ago, there was a step-by-step process that took me through every single action with screenshots included when appropriate. It was exponentially helpful. I was so lost without it this time around, and I was wondering if I could access it again in the future if needed.
The following is a blurb from my conversation with Sanjit tonight:
Sanjit: You have purchased Muse subscription , correct ?
Sanjit: or Creative cloud >
Sarah Rushing: Yes, we purchased Muse for 1-year, as well as Business Catalyst for 1-year
Sanjit: Perfect
Sanjit: With Muse you get 1 free site , so once you create a site and then publish to BC. In admin console you launch the site, that makes your free count used. Now if you create another site, then system asks you to upgrade the site to a paid site plan. ut when you delete the previous site then the free count becomes free and can be used for any other site
Sarah Rushing: Yes, that is what I did. Is this what I need to do each time? Because I am concerned that the email and website will be disrupted every time I need to make slight adjustments to the website?
Sanjit: No, you dont need to do that everytime. If the site is scrambled everytime you publish then please report to us. Thats not the ideal way for solution.
Sarah Rushing: Well Sanjit, I can tell you right now, that is how it has been functioning since we bought the program. I am not entirely certain, but I believe we bought Muse and BC in January.
Sarah Rushing: I can absolutely guarantee you that the site will inevitably scramble. Am I the only customer you have heard of to have this issue?
Sanjit: Yes, i have not seen any other reports for this issue
Sanjit: Well this needs a deep investigation
Zak, anything that you could offer for clarity of process, would be incredible. I don't know if you will have time to look at this before Monday, but I can tell you I will be available at a moment's notice to fix this issue and to learn anything about Muse and Business Catalyst that you have to offer. Thank you for your time, and I hope you have a wonderful weekend.
Sincerely,
Sarah Rushing
I'm concerned that no one will really read this because it is so detailed and boring and comprehensive, but it is absolutely critical that I find a proper solution before the next update to the website. Thank you so so much to anyone who can possibly provide some insight into this issue.
Sincerely,
Sarah Rushing

Answer 1

In case anyone is experiencing the same issue, I am trying this today.
Sachin: Okay Sarah, so is it everytime you try to republish the website, it gets scrambled?
Sarah: Yes, that is correct. And the solution thus far was to publish to an entirely new site, meaning delete the existing one on Business Catalyst and transfer the domain information.
Sarah: The last time I did that I experience a slew of issues that resulted in no website and email for 4 or more days. My boss was very angry.
Sachin: Sarah, can you publish your site as a new trial site once.
Sachin: And provide me the URL.
Sachin: Then republish on the same trial site and let me check the results.
Sarah: If I updated the published site within the period of a day, it will be fine. It is when I update the next day or later than that, then the website appears scrambled. So I can create a trial site for you, but it will behave normally for now.
Sachin: Sarah, while republishing the site, did you select "Only modified file" or "All files" while publishing?
Sarah: I tried everything.
Sarah: I made a few changes to my argponline_4.muse file on September 4th, 2013. The published website at that point was argponlined.businesscatalyst.com (D). The domain name was argponline.com . (D) was published probably about two months previous, maybe longer ago. When publishing (D) on September 4th, 2013, the website appeared scrambled. I tried to publish only modified files, as well as publish the entire site, as well as close programs, and restart the laptop. I decided to follow the advice given previously, and I published and launched argponlinef.businesscatalyst.com (F).
Sachin: Okay. there is one  more thing I would like you to try.
Sachin: Publish a site as a trial site.
Sachin: Then wait till tomorrow.
Sachin: After that login to the admin panel of the site.
Sarah: Okay
Sachin: There go to Site Manager>File manager
Sachin: There will be a file there named Muse_manifest.xml
Sachin: Delete that file and then republish the  site from Muse.
Sarah: So in the Adobe Admin Console, underneath Site Manager, I see Web Forms and System E-mails. No file manager?
Sachin: Please hover the muse on your name at top right corner and click  on My details.
Sarah: Okay, yes.
Sachin: Now scroll down  and check the option that says Enable online content editing (incompatible with Muse)
Sachin: And  then click  on save.
Sarah: What does this do, and why does it say it is incompatible with Muse?
Sachin: It will help you see  other options in BC.
Sarah: Okay, thank you.
Sarah: I see the File Manager now
Sachin: Okay.
Sachin: Now select the file named Muse_manifest.xml
Sachin: And use the delete button on the right side.
Sachin: but do it tomorrow
Sachin: With a trial site
Sachin: Not with  the live site.
Sarah: Okay, could you please explain to me what deleting that particular file is supposed to do? I am just very interested in how this works.
Sachin: This file contains the information about your last upload.
Sachin: Deleting it will make sure that "ALL" the files are uploaded again from Muse.
Sarah: Okay, so:
Sarah: I will publish a trial site.
Sarah: Wait until tomorrow.
Sarah: Publish again. If I have an issue, I can log-in to the admin console for this particular trial site and go to Site Manager --> File Manager, and delete muse_manifest.xml.
Sachin: I will create a case for you and you can respond to the case.
Sachin: Correct.
Sarah: After that, I will try publishing again and see if it resolves the issue.
Sarah: That would be great, thank you Sachin.
Sachin: Thank you for contacting us. Have a Good Day!