Virtual Channels File changes

I've been re-encoding my entire library and as a result I'm replacing big portion of my collection that I also happen to use for Virtual Channels.

If I have a show added to Virtual Channels say Friends for example and on my back end media the files change.

Was: Friends S01E01 1080p h264 AC3.mkv
To: Friends S01E01 720p h265 AAC.mkv

Is there anything I need to manually do in Virtual channels to reflect the change. Library scan? Prune Media?

Interested to hear the "correct" way to do this as well because I am also venturing down this path (compressing some of my DVD rips). I noticed that when I did this with a show I was watching, it lost its watched status for that season (outside of the Virtual Channels). Wasn't sure if that was because I removed/pruned before refreshing the library.

So, I started doing: 1) dump the new files into the same directory of the other files (now you'll have 2 S01E01 files) 2) scan media in Channels (now you have 202 episodes instead of 101) 3) manually remove old files from folder 4) prune media. No idea if that's a better method or not.