Plex doesn’t modify the recorded files or create new XML files. The XML info I’m referring to is pulled from the Plex database. The document I linked describes this, but if you “Get Info” for an item and then select “View XML” from the bottom-left of the dialog which opens, you can see its XML info (sorry for the repeated links, they’re created automatically by the forum). The XML file from your screenshot is the one created by NextPVR; Plex doesn’t utilize it in any way.
You may want try the Plex Dance on an item recorded with NextPVR to see if that triggers the detection (when it’s added back). If not, try a manual analysis afterward. I’ve not got anything particularly special going on on my system; but, for what it’s worth, it is a Linux-based server. It should behave identically on Windows however.
My DVR library on this server currently has only one top-level directory. However, when I initially set it up, I had two directories (one for my Plex DVR stuff, and one for the thing recorded by NextPVR. It worked fine either way. I’ve tested beyond two directories, but have no reason to believe it would cause any issues.
