I had 3 documents in 3 Indesign files. They are separate publications, but I wanted them in an Indesign book to generate an index that covers all three volumes. Everything going well - I was on the final edit - when file 3 lost the little blue marks that indicate index marks. They were there - a search for index markers went to where they should be, but I could not see them (no, it wasn't a change in the view.) Solved the problem by deleting the book file and copying and pasting file 3 into a new file, in a second new directory. Boom, could see the marks. Went back to editing, checked that all 3 files were fine. One of the things done last was moving the page numbers on the master pages from the bottom to the top of the page in all 3 files, which turns out to be a quick way of verifying the files.
Held my breath, created a new book file (with a different name) in the new directory and made sure I put the files from the new directory in it. Do NOT have to sync the files (that was done long ago). Checked the books - everything was fine. Generated the index into a separate file in the book, replacing the old index. When that was done, I saved the index, saved the book, closed the program.
Opened the program, checked the index, and then opened one of the files. It was back to the old (first) version of the file. All my edits gone in all 3 files. If I open the 3 files without opening the book file, I have the final versions. The index is NOT accurate for the new version.
What do I do? The best thing I can think of is to uninstall Indesign and reinstall it, moving all the wrong version files off the hard drive. Then I can make a clean version of the book file and generate a good index. Or is there something I am missing?
I don't mean to accuse you of anything here, but this sort of problem nearly always turns out to be some sort of user error, typically having multiple copies of the book file in diffeernt locations and opening the wrong one. This can happen easily if you don't check where the book is being saved and it winds up in a folder you didn't intend (typically the folder for a project you were also working on previously). Make sure you do a file search to locate all copies and check the time stamps.
This happens to pretty much everyone at some point, many of us more than once.