In the DVR settings there is an option to automatically skip ads/commercials when recording. This is a great but risky time saving feature. If the algorithm gets it wrong, then there is no way to recover lost parts of the recorded show.
I don’t know if this is technically feasible, but to me a much better solution (or new additional option) would be to insert DVD-style chapter markers after each series of ads before the show resumes. In this way, I can press the Skip forward button on my remote and skip all of the ads that Plex detected.
If Plex got the detection wrong, no worries - I just manually rewind or fast-forward to find the correct location.