You didn't tell what specific symptoms of damagedd filesystems did you encounter. This warning could be nothing. When you get it, there should be a checkbox enabling you to scan without repair, then you scan your pendrive and answer a question if any files are damaged at all. You can always ignore that requester and run chkdsk manually disabling repair. (start -> run -> CMD.EXE then type
chkdsk <drive>, and it will run without repair).
However to answer a question if you lessen your chance of recovering - noone will tell you for sure. If the drive's cell is at it's limit, you will get read errors while copying, but after running chkdsk you will be able to copy a file without problems. I bet though it will not be complete. Other letdowns I've faced in my life include chkdsk making complete mess of my FAT, making my filenames look gibberish. Also look what I've faced on one SSD drive, which I'm still not sure whether it is responsible for this mess.
I always first run chkdsk without
/F then eventually with it. Not trusting that thing. Also I've gotten into a habit of copying things to pendrives with checksums (CRC32) made by TotalCommander (shareware) or a batch file using fsum.exe (free). Assessing file integrity is trivial then.