No the Plex Dance is a specific set of instructions (see linked article). Plex has features to attempt to detect file moves/renames. Sometimes its something we want to use, other times (In cases of bad metadata) its not something we want.
Doing the plex dance in the exact order is important, it will first remove, and purge any records plex has for those files, and then will re-scan/identify the the files hopefully correctly,
/volume1/Media/TV shows/@eaDir/Eureka Season 3 disk 1.mp4
does not follow the naming schema.
/volume1/Media/TV shows/Eureka (2006)/Eureka S03E01.mp4
is the correct format