Those were all created at a time where the only way to add a custom level was to replace an existing level (mostly Burnside).
They can be converted manually but it's a time consuming job. Until they get converted, you can still play these levels by running thugpro, copying the custom level files into AppData\Local\THUG Pro\data\pre, which replaces the original level files, and load the original level from the official level menu list.