I used to do book work, but it's been a few years and I'm not sure I understand your problem.
…indicating a change had been made in a copy of the original file.
Does that mean that you had a book file that had certain InDesign files as it's chapters, but now that book file has other InDesign files as it's chapters (and it sounds like you might mean copies of the original files). If that's so, you could remove the chapters from the book file (the copies) and import the ones you would rather have (the originals). I don't remember if it's necessary to undo the section starts of the chapters after you remove them from the book, or if the book will redo them once you import them back into the book, but keep an eye out for that if the pagination doesn't work. You could also just create a new book file, but make sure the InDesign documents you import aren't part of another book at the same time.
Then again, I could have read your question incorrectly, and if that's the case, maybe you could tell me where I got it wrong.
When you import files into an INDB book file, those are NOT copies, those are the original files. When you do changes the originals are changed.
You have to go back to your last backup, no other solution is possible.
I would recommend working on a DropBox drive or similar as these cloud solutions have a regular backup where the user can step backward and restore a former version.
Of course, any other local solution might also help like Apple’s TimeMachine regularly applied.