If you don’t follow the documentation, then Plex may work, until it doesn’t.
Start by adding correctly named season folders for the show. That takes maybe two minutes.
Per the docs, .
is a valid separator, so you don’t have to replace them with spaces.
Plex should ignore everything after sXXeYY (ex: it ignores episode names), so you may not have to remove the extra info.
Performing the Plex Dance, if needed, takes a few minutes.
You can also try resetting permissions. Synology will sometimes mess them up. See FAQ 29 - DSM 7 - Give PlexMediaServer access to your media. Follow the process even if they look OK in DSM.