Message filters are stored in account subdirectories in the file msgFilterRules.dat, which is an ordinary line-oriented text file that can be edited outside of Thunderbird (when Thunderbird is not running). Its format is obvious for the most part, and it's fast and easy to do things like change all "Move to folder" to "Delete" in a particular line range, for example, if you have a good enough text editor. I assume you can mark lines to be ignored rather than delete them. What is that mark?