In my library, I've imported the DuckTales episodes from the original run, as well as many episodes recorded from the 2017 reboot.
I have them organized in 2 separate folders, the original is "DuckTales/Season_XX/DuckTales.SYYEZZ.mkv" and the reboot is separated by being in its own folder "DuckTales.2017/Season_XX/DuckTales.2017.SYYEZZ.mkv"
Channels DVR matched them all as episodes from the 2017 reboot. I went through and selected all of the 1987 run (using the newly provided folder display option to help me differentiate), and tried to select "Fix Incorrect Match" and then give it the correct option in the list of presented options under DVR/TV Shows. It proceeded to change the match for all of the episodes in the list (including the 2017 episodes that were matched correctly).
I tried to select "Fix Incorrect Match" on an individual episode's drop-down menu, but this appears to be searching for only episode names in the currently matched episode title/series.
I don't think I have a way, in the current UI, to fix the match state so that the episodes are broken apart into 2 separate matches in this case.
Edit: I did find a way to work around. I moved all of one the (manually) incorrectly matched episodes to the trash, then adjusted the folder location of the 2017 version, where I could then force an import refresh. Channels DVR matched those to the 2017 version, then I had to go through and pull the 1987 version out of the trash one-by-one, to restore them to the library correctly matched. There's gotta be a better way.

