Interesting behavior on booting back to my main system drive. I wasn't getting mdworker errors related to "phantom" ids.
I manually started Time Machine to see if I could trigger errors. It appears that running on another boot drive for a day changed enough files that Time Machine could not used it's cached scans. From logs:
Oct 31 20:31:27 Mac-Pro-2.local com.apple.backupd[929]: Starting manual backup
Oct 31 20:31:28 Mac-Pro-2.local com.apple.backupd[929]: Backing up to /dev/disk11s2: /Volumes/DroboTM/Backups.backupdb
Oct 31 20:31:32 Mac-Pro-2.local com.apple.backupd[929]: Event store UUIDs don't match for volume: Hitachi 2TB
Oct 31 20:31:32 WMac-Pro-2.local com.apple.backupd[929]: Event store UUIDs don't match for volume: Seagate 4TB
Oct 31 20:31:32 Mac-Pro-2.local com.apple.backupd[929]: Event store UUIDs don't match for volume: WD Black 1000
Oct 31 20:31:32 Mac-Pro-2.local com.apple.backupd[929]: Forcing deep traversal on source: "SanDisk240" (device: /dev/disk0s2 mount: '/' fsUUID: 31D86B38-3F77-30C7-B2AC-8E0274C41535 eventDBUUID: 235CDDDF-EDF3-40C4-9C10-2B11DD9CBEE8)
Oct 31 20:31:48 Mac-Pro-2.local com.apple.backupd[929]: Deep event scan at path:/Volumes/Hitachi 2TB reason:must scan subdirs|new event db|
Oct 31 20:31:48 Mac-Pro-2.local com.apple.backupd[929]: Unable to use cached scan; fsevent uuid mismatch
Oct 31 20:31:48 Mac-Pro-2.local com.apple.backupd[929]: Running event scan
Oct 31 20:32:29 Mac-Pro-2.local com.apple.backupd[929]: Finished scan
Oct 31 20:32:29 Mac-Pro-2.local com.apple.backupd[929]: Saved event cache at /Volumes/DroboTM/Backups.backupdb/William’s Mac Pro (2)/2014-10-31-203132.inProgress/EC26B84B-A5EA-4C88-829E-27733E985103/.CF113335 -FFC3-394A-B363-1A0B068CB412.eventdb
Oct 31 20:32:29 Mac-Pro-2.local com.apple.backupd[929]: Not using file event preflight for Hitachi 2TB
Oct 31 20:32:33 Mac-Pro-2.local com.apple.backupd[929]: Deep event scan at path:/Volumes/Seagate 4TB reason:must scan subdirs|new event db|
Oct 31 20:32:33 Mac-Pro-2.local com.apple.backupd[929]: Unable to use cached scan; fsevent uuid mismatch
Oct 31 20:32:33 Mac-Pro-2.local com.apple.backupd[929]: Running event scan
Oct 31 20:32:36 Mac-Pro-2.local com.apple.backupd[929]: Finished scan
Oct 31 20:32:36 Mac-Pro-2.local com.apple.backupd[929]: Saved event cache at /Volumes/DroboTM/Backups.backupdb/William’s Mac Pro (2)/2014-10-31-203132.inProgress/EC26B84B-A5EA-4C88-829E-27733E985103/.0DC0DAA8 -2F46-36FD-9A05-638EF4172DD7.eventdb
This was repeated for all backed up drives.
I still have some time to go (somehow it found 46 GB of material that needed backup), but hopefully this cleaned everything out.
The one error I am getting consistently is
Oct 31 21:51:48 Mac-Pro-2.local mdworker[1217]: code validation failed in the process of getting signing information: Error Domain=NSOSStatusErrorDomain Code=-67062 "The operation couldn’t be completed. (OSStatus error -67062.)"