I think a lot of people have the modern files installed because they were our first user-created major add-on, so we gave them a spot in the automatic updater.
Because they were in the automatic updater, there were a lot of users who just downloaded everything that's there, and ended up with the Modern files - it's even easier on the iPad - there were only two update options listed, so I think a lot of people just installed both.
Eventually (I think it was a year or so ago), we decided to remove the modern files from our own updater, and let the community files handle those, but there's nothing in Hero Lab that prompts people to remove them, and they're no longer automatically receiving updates after that. Now, in the most recent update, there was a change in the Pathfinder files to improve a piece of the editor, and that change means that a bad way of coding something that was used in the modern files is now a forbidden way to code things. That's why the error is popping up now.
P.S. The change that was made was; if you chose specific weapons to grant proficiency in, for a class, for example, the list of weapons to choose from included many things that didn't belong there, like every type of ammunition, all the specific weapons, and all the headers, which cluttered up the list. Now, ammunition, specific weapons, and headers no longer generate WepProf tags. The Modern files had some cases where WepProf tags from weapons that were set as headers were being used in some fashion. Because those tags are no longer generated, it's no longer legal to use them, and that's the source of the errors.