The SysData directory contains the reports and components. Back it up. Don't forget offsite storage. And don't forget to test the restorability of the media. While this won't exactly prevent corruption, it does prevent disaster.
 

Compact the spec set(s) regularly. This creates a new, clean file with the same structure, and this is less likely to cause errors or a loss of data. Shoot for weekly if FRx is being used regularly.
 

Keep spec sets to a reasonable size. If too large, consider creating a new spec set. Then move some reports into it. Be sure to compact the original spec set after moving reports.
 

After making changes to a report catalog, always SAVE the changes before generating the report.
 

Finally, exclude the FRx SysData directory from network virus scans.