I am running InDesign 16.4 (Mac Big Sur 11.5.2) and working on two publications. I have had the same problem on both publications. I have received errors multiples time that say the changes cannot be saved and the file will need to be repaired. It saves a recovered file but loses my recent work. I chatted with someone at InDesign and she said I need to save the file to "Downloads folder" because of a software problem and not to save to "Documents". I tried that and it still happened. Could it be a preferences issue, font issues...? Please help. Thank you.
One standard troubleshooting step would be to open the file(s), and see if you can Save As in .idml format. Then re-open and see if new edits can be saved. This can clean out file "gunk." Also, do you have documents that this does not occur on? What happens when you create a new doc, type something, then try to save?
I opened a new doc and typed and also placed a pdf and it seemed fine. Then I saved the publication doc that I was working on as .idml like you suggested and then reopened it and InDesign crashed.
So its definitely when I go to Save my document. I get the message "InDesign is having difficulty in reading some unsaved changes in "filename". It may damage the file. Would you like us to try and repair the file? Some unsaved changes may be lost." Then I Save As and usually it crashes.