This is difficult for the forum—as fellow users—to diagnose as most likely it relates to your system and your notes. I’m not aware of a general problem with watched folders and notes.
As Tinderbox’s ‘watch’ is one way - it just generates copies of the currently watched notes, you could try deleting the current watched folder, then saving and closing the TBX document. then re-open and re-watch Notes. If the problem persists, it may be a problem within your Notes infrastructure. to be clear, nothing your doing is wrong, but there may be a hidden gremlin in your Apple Notes data. Another factor is whether you use the iCloud or not. aAt that point it might be better to contact formal Tech Support (
info firstname.lastname@example.org) as a closer look at you TBX may be required. [Edit: fixed email address to use one recommended below by @eastgate]
Also as a general point. For issues like crashes, if it’s urgent, I’d suggest contacting support as well as posting here. This is a user-to-user forum, so we can’t see under the hood of the app so those sort of issues are harder to advise upon.