If you have a recent backup, rename it (so it doesn't immediately replace the original) and restore it. Check the restored PAF file, and if it is good, it becomes your new main PAF file. If the restored one is bad, follow the same procedure in restoring successively older backups until you get one that is good.
Note who is absent from the restored file when compared to the one you have been using. You can use the File menu in PAF to open one file while the other is still open. Then select Tile Vertically from the Window menu to show the two files, and click the Individual tab in both PAF windows. Now you can compare the two files, name-by-name.
A faster but less precise approach is to compare the highest RINs and MRINs in the two files, since that is where the most recently added people can usually be found.
Then you can export them in a gedcom, taking careful notes of how they connect to other people. Lastly you will connect them to the proper places in their families.
If you don't have a backup, try exporting All of the file, and then importing it into a newly created PAF file. (Give this file a different name than the other one.) Then see if the problems are still there.
You can try running check/repair on your files too, but the condition you are describing is probably beyond its capability.