Usually, the purge command is used to remove filenames
omnidbutil -purge -filenames -force
But this is also done as part of your normal daily Maintenance, which runs every day at noon, so, there is probably no need to do thsi manually
Good idea to address the IDB backup issue. I wish I had a nickle for every time someone has a catastrophic IDB failure, either doesn't have a IDB backup, or doesn't know where it is. I have to tell them "Start Importing media until you find it", and I really don't enjoy doing that