I was under the impression that if I removed this plugin, that the players would have the blueprints unlocked that they had unlocked prior to installing this plugin, but it appears that is not true? If I decide not to use this plugin, I have to wipe the plugins or else they will remain unlocked?

Not from what I've seen It seems to unlock them for a player as they connect to the server. They stay if the plugin is unloaded on my server.