Not re-recording episodes I have

Using Plex as my DVR and MCE I did some changes to use MCE to scan-remove commercials, but I changed the format to MKV file instead of using MP4. Getting alot of dupes can MCE scan what we already have recorded so it skips over adding more to my FOLDER?

MCEBuddy won’t convert already converted files unless remonitoring is enabled in the monitor task expert settings. Screenshots or log files would help