TOC stopped updating properly...

Hello - I'm having an issue with my Table of Contents. It has stopped updating properly. I have a 90+ page manual where I had the TOC working fine. I have been saving revisions of the manual when edits were made. The issue is that when I go to Update TOC, it clears the entire TOC of all the headings for the main body content. It keeps the "title" and the "Index" heading which happens to be the last entry for the TOC (this heading/page is not threaded with the rest of the main body).
I went back and looked at TOC for previous revisions, and I changed something 2 revisions ago and since then the TOC stopped working. The only significant format change I can remember is that the TOC originally was not threaded in with the main content of the document. Looking back a couple of revisions ago I had gone in and threaded it to the main body of the document. By the time I realized there was an error occurring I had saved yet another revision. But in this last revision I went in an unthreaded the TOC from the rest of document but it did not correct the issue. Needless to say, I have made several edits within the document that I haven't necessarily tracked (grammer, spelling). So going back several revisions to the properly working TOC would require re-edits of that revision....something I'd rather not have to do.
I'm using 3 levels of Section Headings/Paragraph Styles in my TOC --- and i've gone into the main body and those headings are still properly set as their respective paragraph style. I've even tried creating a completely NEW TOC in my latest revision with just one paragraph style and nothing comes up in my TOC. Its like nothings there or it can't see the tagged style in the document, but I know it is there.
Any ideas? Please help.
THANKS!

Hallelujah! I believe I've fixed it. Thank you to whoever added that "more like this" box on the side of the forums! And for the following forum post from 2008. Ain't the internet grand?
This appears to have fixed the issue: http://forums.adobe.com/message/1313052#1313052
I knew through my back revisions it was a threading issue. So I followed the above poster's advice and I basically CUT my entire manual and then deleted all the empty pages. Added 2 pages back and then pasted my content into those pages. Tested the TOC and when it asked me If i wanted to include overset text I knew I'd fixed it and that it was looking at all the headings. The whole content came up just like its supposed to. Then I added 90 more pages and expanded the thread back. All seems to be good.
Do NOT put TOC in your threaded story. Not cool. I had it right at first and then put it in there ---- that's what screwed me up.
....now back to work!

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