Besides all the other excellent suggestions you’re getting here, I read something in another thread just now which might help, be something to consider:
https://forum.literatureandlatte.com/t/long-save-times/127117/7
The discussion is about using Save As, rather than Save, and you can see that this is often done mistakenly, and with results that aren’t understood.
If this happened to be your case, you could have been making your additional inputs to the project in a different copy than the one you’re looking in now. So you’d need to find that…
May not be your issue, but you can consider it.