Over time... a lot of cruft can build up...
1) Backup User Data to another machine - this is pretty important - as the next steps will wipe out the NAS
(if you don't have QFinder - download it now for Mac/Windows - if your primary platform is linux, find a Mac/Win box to sort this)
Once that is done
2) Once all user data is backed up - shutdown the NAS
3) Pull the drives - this will force the next step
4) With the drives pulled - start the NAS up
5) Fire up QFinder once the NAS is up -...
Rebuilding a QNAP NAS