Problems with RH 9, CBT, and Printed Documentation

When I upgrade an x5 project in the new RH9, all appears to go fine until I try to generate the Printed Documentation. I was disappointed that the printed documentation STILL requires so much cleanup. Text tagged with the Online condition sometimes displays on some topics, even when Online is excluded from the output. Also, some of the cleanup issues surrounding headings and index entries are still necessary.
The four biggest issues are:
1) If a "book" TOC heading also has content (a topic associated with it), a double-heading appears in the printed output. You have to manually remove all these extra headings in the cleanup process.
2) All index entries appear in the paragraph BEFORE the actual heading they mark, instead of after the heading, resulting in the Index not being correct (if a heading appears at the top of the page, the Index points to the previous page where the index entry resides, instead of the correct page). I have to manually go through the entire document and move each index entry to the paragraph AFTER the heading it marks.
3) Robohelp ignores the exclusion of Online conditions on some random topics. There is a workaround to "trick" Robohelp, but it takes *a lot* of time to do. To "trick" Robohelp, I had to generate a printed manual and make a list of all topics that "slipped" through. And, then edit each topic where the online condition was ignored, by adding an extra, empty paragraph to the end of each topic that had:
·         a single paragraph of text (aside from header and footer info)
·         ends with bulleted list (and no extra paragraph marker following)
·         ends with a table (and no extra paragraph marker following)
·         ends with a figure (and no extra paragraph marker following)
·         ends with see also\How do I\misc button text (and no extra paragraph marker before the seealso/how do I listings)
4) I noticed that when I opened a topic for the first time in Robohelp, the Online condition sometimes gets applied to incorrectly tagged text (it wasn't tagged this way in the x5 content).  This requires me opening each topic in the upgraded project, and checking each topic to make sure the online condition is applied correctly in each one (a very tedious process, especiallly if you have a doc set of over 1 mil words!).
Expected results:
Printed doc does not contain double headings. Index entries appear after headings. Conditional text behaves as it is supposed to behave (and if you tell Robohelp to exclude the ONLINE condition, it does it for ALL topics).
Does anyone have any suggestions/recommendations for this? Yes, I have the latest build. We held off on upgrading to previous releases of Robohelp because of the Printed Manual problem too (it seems like each version created more clean up work). :-(  I logged a bug on the Adobe forum.Any and all suggestions appreciated.  Thanks!

Mr. Grainge,
Thank you so much for your thoughtful answers back!  I appreciate you taking time out to write such a thorough reply. I hope Adobe appreciates you!  You're number one in follow ups!
Unfortunately, your answers did not solve my problems. But, you did give me some ideas on where the problems could be occurring. So, thank you!!  Before I begin: In answer to your question, yes I *am* using the supplied Style Mapping template (I never had luck with the custom one myself). Also, I am going to hold off on replying to 1) and 2), but I'd like to share my answer on 3) and 4), which is really just what I need to get Printed Documentation working in Robohelp 9 the same way it worked in x5.
A little history:  I have a set of about 50 help projects that span many versions of our company's product, and multiple versions of Robohelp (some even go back to the 90s!). They even include some help projects that were originally in Frame/WebWorks but were later ported to Robohelp. There's a lot of history to them.
Investigating the Problem: When I opened an x5 project in RH 9, I noticed that some of the timestamps on the .htm files didn't match the rest of the files. It turned out, that these very same files that were the ones giving me problems with the Conditional text!  That's when your thoughts about the mapping came to mind...As I said, my project spanned mutiple versions of Robohelp. I wondered if some of the coding on the .htm page was being parsed incorrectly on upgrade, and if if that was the reason why RH couldn't update the pages (which explain the unchanged timestamps). In other words, I wondered if Robohelp was mapping the styles correctly on import. So, I compared these unupgraded .htm files with ones that did upgrade, to see if there was something on the code page that could be causing the problem.
Solution to Fix 3) and 4) above:
I'm going to list out everything that I did below, however, not everything on this list applies to everyone. But, hopefully it will help you, if you ever run into this scenario yourself, and it might give you some ideas on how to get your HTML files working. So, before upgrading, here is what I did:
I opened my old CSS in a text editor and removed all the Robohelp autogenerated comments.
In Homesite, I did a bunch of Search and Replaces on a copy of the older x5 project.  I looked for code that may have been generated in an earlier version of RH,and for unusual structures in the meta and style declaration area that could be causing conflicts. Here is a list of my search and replaces below:
Search for:
<!--(Title)=========================================================-->
Replace With:
nothing
Search for:
<!--(See Also)======================================================-->
Replace With:
nothing
Search for:
<!--(Content)=======================================================-->
Replace With:
nothing
Search for:
<p> </p>
Replace With:
nothing
Search for:
<p> </p>
Replace With:
nothing
Search for:
<html>
<head>
Replace With:
<html>
<!--(==============================================================)-->
<!--(Document created with RoboEditor. )============================-->
<!--(==============================================================)-->
<head>
Search for:
<!--(Meta)==========================================================-->
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
<!--(Links)=========================================================-->
<link href="MyHelp.css" rel="stylesheet" type="text/css">
<!--(Scripts)=======================================================-->
<script language="javaScript" type="text/javascript" src="MyHelp.js"></script>
<script language="javascript" src="eHlpDhtm.js"></script>
</head>
<!--(Body)==========================================================-->
<body TABINDEX=1>
Replace With:
<!--(Meta)==========================================================-->
<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
<meta name=generator content="RoboHELP by eHelp Corporation - www.ehelp.com">
<meta name=generator-major-version content=0.1>
<meta name=generator-minor-version content=1>
<meta name=filetype content=kadov>
<meta name=filetype-version content=1>
<meta name=page-count content=1>
<meta name=layout-height content=597>
<meta name=layout-width content=662>
<!--(Links)=========================================================-->
<link href="MyHelp.css" rel="stylesheet" type="text/css">
<!--(Scripts)=======================================================-->
<script language=javaScript
  type="text/javascript"
  src="MyHelp.js"></script>
<script language=javascript
  src="eHlpDhtm.js"></script>
</head>
<!--(Body)==========================================================-->
<body TABINDEX=1>
Search for:
<a class=toplinks href="#top"> Top</a>
…or…
<a class=toplinks href="#top">Top</a>
Replace With:
<a class=toplinks
href="#top">Top</a>
Search for:
<h3 id=SeeAlsoTitle
class=SeeAlsoTitle
style="x-condition: Online;">See Also</h3>
<div id=seeAlso
Replace With:
<h3 id=SeeAlsoTitle
class=SeeAlsoTitle
style="x-condition: Online;">See Also</h3>
<div id=seeAlso
After I did these all these search and replaces in the copy of the x5 version of the project, I opened the project again in RH 9 and upgraded it.  After the upgrade, I checked the timestamps on the .htm files to make sure they all changed.  They did!  It worked!  Everything upgraded properly this time... I tested the Printed Manual output and no conditional text slipped through this time. Yay!
In Summary:
This is what I learned if you are having problems with Conditional text and Printed Manuals in an upgraded RH project:
Always make backups of your older projects before you upgrade anything. I know this is elementary, but I thought it was worth reminding.
Check the timestamps of the files after you upgrade the project. If there are a group of files with timestamps that aren't similar to the rest of the files, chances are Robohelp was having trouble converting those files.
Try looking at the HTML code in those files and see if anything looks out of the ordinary. Some examples are above.
If you have already ported the RH project and it's too late to go back, go look at the file timestamps anyhow. For all the older files, try opening each one in Robohelp and add a space or something (to force RH to change it), and save it. I didn't have the time to verify this, but it seemed on most instances: when I forced RH to save the file manually, it updated correctly and the problem with the conditional text went away.  (This option takes longer, especially if you have to do each page individually, but it's worth a try, IMHO.)
Aside from the initial Printed Manual woes, which are resolved, the upgrade process from RH 9 really was seamless!  Best I have ever seen!  Everything just works!  Awesome is a word that comes to mind.
Printed Documentation output does work on upgrade, but in my opinion is: it is no better than it was before, in previous versions.
I wish there were more fixes to the Printed Manual output. When you have a product help system that spans multiple versions, contains over 2.5 million words, and 10,000+ topics, having a lot of cleanup on the production end is costly. What use to take a person on my team less than a day to generate 50+ PDFs in FrameMaker, takes 4-5 weeks man-time in RH.  I will outline my opinions in my next reply to this thread.
Thanks again, Mr. Grainge!

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