If your file is clean, back it up using a unique name.
If it isn't clean, an old but useful procedure is to export ALL the data to a gedcom file. Then create a new PAF database file and import the gedcom into it. Run check/repair again. Chances are it will be reported as clean, in which case, back it up with unique name.
If there are still issues, take a copy of your file to someone who has PAF Insight and have them open it in PAF Insight and save it under a different name. Then at home, open the file created by PAF Insight in PAF and run Check/Repair.
Sometimes the free version of Legacy6 can fix database problems (www.legacyfamilytree.com). It can open PAF files directly, but can only export as gedcoms.
Let us know how things went. Hopefully the import-export trick will clear up any problems.