TV is not included in the MC for Linux feature set, so I cannot use the "clean up time-shifting folders" tool there.
I had to stop using the TV feature due to my region going encrypted so it is disabled on my Windows machines.
As a test, I re-enabled the TV feature on my Windows machine and ran the "clean up time-shifting folders" tool, yet according to the log it did not remove the offending stale database entries.
0011391: 8488: Import: GetNewFiles: Searching: M:\TV\
0011453: 8488: Import: GetNewFiles: Searching: M:\Movies\
0011516: 8488: Import: GetNewFiles: Searching: M:\Downloads\Complete\
0011578: 8488: Import: GetNewFiles: Finish (4953 ms)
0011578: 8488: Import: GetMissingAndUpdateFiles: Start
0011578: 8488: Import: GetMissingAndUpdateFiles: Getting files
0011578: 8488: Import: GetMissingAndUpdateFiles: Sorting files
0011578: 8488: Database: CMediaInfoArraySort::Sort: Files: 621; Elapsed ms: 2.062
0011578: 8488: Import: GetMissingAndUpdateFiles: Looping 621 files
0011641: 8488: General: CFileSystemManager::AnalyzeDrive: Drive does not exist (drive: F:, filename: F:\TV Recordings\6-1 WBRC 2012-02-19 22-7\6-1 WBRC 2012-02-19 22-7 - Saved Time-shifting.jtv, type: 1, attributes: 4294967295)
0011657: 8488: General: CFileSystemManager::AnalyzeDrive: Drive does not exist (drive: Q:, filename: Q:\Video\JRiver\TV Recording\6-1 WBRC 2015-09-20 15-44\6-1 WBRC 2015-09-20 15-44 - Saved Time-shifting.jtv, type: 1, attributes: 4294967295)
0011657: 8488: Import: GetMissingAndUpdateFiles: Finish (79 ms)