Thank you for taking an interest in this, I too find it very curious. I do feel a bad for hijacking the thread though and I'm not sure how helpful I can be with answers since it was a few days ago and I'm not sure how many saves etc I did, but I will try my best to provide as much info as possible below:
I can't remember if I copied and pasted the text in. Now that you mention it, I'm pretty sure I placed it.
The total document now has 442 pages (so that's 442 linked frames) with 3 different master layouts (But I think at the time the file was that size it would have been at about 263 pages).
I solved the overflow by a series of clicks - frame by frame - because I needed to apply different formatting for the chapter pages so chose to do this as I went.
Two of the master layouts are chapter header pages. I didn't use images here though, only symbols and same for the ornaments which I know some authors use images for.
In terms of the number of styles, I was working with two main styles - one for the body text, and one with a dropcap for chapter pages. Then a single character style for italics. The placed text should all have been in Adobe Garamond Pro with no ornaments or decorations of any kind, and no style changes. However I did do a find/replace to apply that italic character style as soon as the text was placed.
In terms of number of saves, I tried to save after every chapter. At this stage I would have been at about Chapter 30. So maybe that's the issue? I had I think two formatting related crashes which were reported by someone in another thread so is a known issue to do with styles. Other than that I would have opened/closed about four - 6 times? So I guess 6 - 10 loads, one place, no deletes, 30 saves?
After I deleted the unlinked text, everything came right. That was already much further in though. For the remaining pages I pasted them in one by one and all was fine.