The option is there, it’s just at the show level, not the season or episode levels:
You may want to have a look at your file names and directory structure for the two series. Since there’s an ambiguous name, you’ll need to include the year, in parentheses, for both series. For example:
TV\ <--- Library should point here, name unimportant
The Flash (1990)\
Season 01\
The Flash (1990) - S01E01 - Pilot.mkv
...
The Flash (2014)\
Season 01\
The Flash (2014) - S01E01 - Pilot.mkv
...
Season 02\
...
Getting everything sorted out now though may require the Plex Dance (after the naming is fixed, if necessary), if you’re unlucky: