After directly editing the Plex database as described here and here, the web UI can show negative values for the number which indicates how many unwatched episodes are in a series.
Screenshot below. Other UI within the player shows episodes played/unplayed status correctly, and the negative values do not show up in the iOS or AppleTV clients, so it seems like an issue that only shows up in the web version.
Those instructions only work if the destination is empty of information related to what you are doing. i.e. Copy one user to another. The destination user’s info must be blank or you end up with duplicates. These duplicates are causing the problem since under normal situations, you should not have duplicate watched information. Go back to an older backup database if you have it, and try again but removing the destination data first. Or you can try to remove the duplicates yourself if you know SQL well enough.