Yeah, I'm running into a similar issue. I wondered if it had to do with the fact that most of the wells on my map were migrated from the legacy mod, so maybe the pipe connections broke during the migration. I haven't been able to catch a well "disconnecting" in the act, so it's possibly something that's happened on subsequent loads post-migration, or mid session.
At any rate, what I've found useful as a workaround is to have a delete blueprint filtered on all the pipe types in whatever mod you're using, and then just mark every pipe on the map for deletion and undo. The act of marking and unmarking seems to correct the pipe connections, though it's a bit of an awkward fix to perform every load.
