I have a episode that has E01 E02, and E03 in it. I think back in the 1970’s the did this from time to time. If I put S01 in front of everything I only get E01 and E02 but not E03 when I do a resync. If I drop the S01 it only displays E03 and drops E01 and E02. Realistically it should care how many E’s I add to the file. Unless there is away to say E01-E03 and it knows there are 3 in one file.
Thanks,
it’s right there as you guessed 
TV Shows Folder > TV Show Name (year) > Season 01 > TV Show Name (year) - s01e01-e03.ext
you can find this described in the support article on how to prepare your media (see “Multi-episode files”):
If you do it the way that works, s01e01e02e03 I think, then when you play episode 01 Plex will play all three episodes and present episode 02 as next but if you play that Plex will play all three again and so on for episode 03. That is a BUG that Plex is unable or unwilling to fix even though Emby does it correctly by playing all three episodes and marking all three as played.
Most people here just label the combined episode as e01 and then label the next actual file as e04. Plex does not care at all is there are skipped episodes. If the metatdata is needed for all three and/or the title needs to show all three tthe episode can be edited in Plex as needed.
Some people use various tools to edit the file and break it into three actual files named correctly but I think that is entirely too much trouble. I do not even bother with the additional metadata as I generally know how many episodes are involved by length.
