Reboot the FMS server.
FileMaker Server performs a consistency check when a file is opened.
if its a huge database it might take a while.
Look at the logs to see if their were any failures.
If no errors and the issue persists then take an affected file off line and run a full recover on it.
Recover produces a log of the results at the end.
See what it shows.
If corruption is evident then export the data from the damaged file into a known uncorrupted backup of the file, destroy the corrupted file and every backup of it, and use the good file going fwd. Repeat for each damaged file in the system.
Do a thorough root cause analysis and implement appropriate mitigation actions.