What I would suggest is using MCEBuddy to remove the commercials and then move the files to a directory used by the appropriate Plex library (e.g. "TV Shows"). (By the way, if you have a PlexPass, "Plex Commercial Skipper.exe" is a renamed copy of the "donator" version of "comskip.exe", which can be used with MCEBuddy after copying it to the appropriate sub-directory of your MCEBuddy install and renaming it.)
Yes I do have Plex pass lifetime. Any tutorials on this. Sorry still pretty new with this. Thank you for taking your time and helping me out.
Also I really don't want to go through all of the re-encoding. Is there anyway to just get the playon server to use adskip on the files it already recorded just on a different hard drive?
If you get the premium version of MCEBuddy, you don't have to re-encode the videos. Just select "MP4 Unprocessed" as the profile when you set up a "conversion task." A conversion task is a long term configuration which allows you to process videos matching different substrings in their file names with different sets of options. For example, you might want to remove the commercials from content recorded via a Tablo DVR (like I do) or HDHomeRun network tuner as well as videos from PlayOn. Another option would be to trim off the beginning of episodes in a series that starts with the main titles (e.g. doesn't start with the common "teaser" or "hook").
Videos which have the chapter markers added via Adskipper only take a few minutes each to be processed when "MP4 Unprocessed" is used.
More details for using MCEBuddy can be found in these two articles:
https://www.howtogeek.com/136470/strip-the-ads-from-your-tv-recordings-with-mcebuddy-2/
https://discussion.mcebuddy2x.com/t/mcebuddy-how-to-get-started-user-guides/22
