Hi Heidi,
Sorry to hear about the troubles. If you're missing some investments from a sub-portfolio, then the *.mm4 file would be the issue. If you're missing some transactions from an investment, then the *.dat file for each of those investments would be the issue.
Do you know the full path/filename of the *.mm4 file you normally open? If you go look at it, what is the date modified time? Was it after you made your changes? (If you've saved it since, then this won't be helpful to debug the problem.) You can check the date modified on the *.dat files too.
Do you store your data files on your hard drive, or are they on a shared resource, that could have maybe been modified? Is it possible someone else also had the same data files open at the same time? FM is not truly networkable, so if multiple people are accessing the same data at the same time, whoever saves last gets their changes saved, and will overwrite changes made by the other open instance. For more on using Fund Manager with multiple users, see:
https://www.fundmanagersoftware.com/faq_multiuser.phpAs a possible recovery option, check to see if Fund Manager made an automatic backup on your last exit. If so, you can restore from that, and it should have all your last changes. See "Options / General Preferences... / Data" for the frequency and location of where your automatic backups are being stored.