How to update bookmarks when merging two PDF files?

We have a company catalog that gets generated once a night. It's three step process:
     Step 1) A raw XML file gets generated from our main ERP software (Microsoft Dynamics).
     Step 2) Then that raw XML file is ran against a stylesheet with XEP to produce a nice professional looking catalog.
     Step 3) And the third step is a script that merges the front and back covers with the main catalog produced in step 2. Each cover is two pages (front and back).
My problem is when step 3 runs it produces a final catalog but all the bookmarks are off by 2 pages because the front cover adds two pages in the very beginning. This post may be premature because up until now I've been merging the PDF pages with a program called "GhostScript" and it allows me to merge them via line command. I'm just now trying out AcroExch.App COM Object for VBScript so I'll see if it works but wanted to fire this out for help to see if anyone has encountered this or can confirm if Adobe automatically updates them for you? When I "Merge" the PDF files through Acrobat Pro they get updated automatically, so hopefully it will work the same way with AcroExch.App Object.   Thanks guy!

I think you might be misunderstanding what I'm saying... we are not performing tasks for non-licensed individuals. We purchased a copy of Adobe Acrobat Standard so we could create a PDF of our catalog. That catalog we then put on our website and let people download it. Since our products change all the time, we generate a new catalog every night. The term "server" is just a place where a script runs, I could have it run on my desktop computer if that's really an issue but I think we're talking semantics. Acrobat is not what produces the main catalog PDF, that is done through XEP when it runs through the raw XML produced by our ERP software every night. The only thing we want Acrobat to do is an automated process to merge 3 PDF files together: Front Cover, Main Catalog and Back Cover. That's it. Are you saying that is against the EULA of Adobe for us to do that?
Now for the bookmark problem, what do you recommend I do then? When I merge all three of those PDF files in Acrobat Standard manually it works perfect. All I'm trying to do is automate that process once every night. I know how to automate with Acrobat, I just can't figure out how to fix the bookmark problem?

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