Trouble with Footnotes in InDesign 5.5

Can someone help?
I am designing a book that has approx. 1000 footnotes. I have the 500+ page book split into 4 separate files to save on memory/file size. My first pass through the design went smoothly, with no errors at all. I am currently working through the author's first batch of changes and the files are freezing up on me almost every page. I am able to "force quit" and not lose anything, but that cannot be good for the file integrity!
I am not able to tell exactly when or why this is happening, except that it seems to have something to do with when InDesign needs to move the footnotes from one page to the next.
The problem is intermittent - sometimes I can work pages and pages with no freezes, sometimes it takes me a half hour to get one correction made! It's making me crazy - and fearful I will never get this project done (without having to completely redesign it!)
Footnotes are a must for this client, so I am actually considering manually adding the footnotes. PLEASE tell me if you know of another way to solve this problem?

Thanks, again, Peter!
Your comment about frames gave me the idea to just delete the troublesome frames as I came upon them and that seemed to work. Delete a page/delete a frame, reflow the text. With that trick, I was able to finish the first round of revisions to the book this morning!
I really (really, really) can't tell you how great it was to get your advice on this!! And so quickly. It kept me hopeful I could find a resolution without having to redesign the whole project - and I learned some new tricks in the process.
Is it OK if I save this email (thread) until I am confident I've moved past this issue? (I'm wrapping up for the day now - but will be back into this over the next week.)
Have as great of a day as you've made mine!
- Jen

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