Thank you Jongware! Luckily I am coming from Framemaker so the actual creation of master pages and styles is second nature to me, and I do have a good user manual template to start from. The tips about wide margins and simple fonts are super helpful and I am sure to have lots of code/commands as content. This is part of my “do everything in InDesign” attempt so I hope to make it work!

Thank you for your post Jongware. I've tried a custom preflight profile and indeed it does show hundreds of outdated cross references. But i have confirmed that all refs are good — it's just indesign that seems to think they are bad.

Here's what happens: I open a chapter file in the book and view the Cross Reference window, which shows little yellow triangles everywhere. I select all references, and click the update icon. Now all the warnings go away; I then save the file but keep it open. I move to another chapter file in the book and perform the same actions, then return to the first file and BAM! all the warnings are back. Additionally, if I simply select one cross-reference and update it — a large portion of the other references pop up with warnings. I have spent 8 hours today trying to find out the right way to update these suckers. I've tried front to back of book, back to front, saving then closing each file. Nothing is working. These !#$^!#@$ cross-references which work perfectly keep throwing warnings and are now preventing me from generating this book, with is otherwise completely free of errors.

I had this problem in CS4 so I upgraded to CS5 thinking it might help but to no avail. Has anyone had anything like this happen before? I feel like I'm running out of things to try. Is there something fundamental I am missing? Help!