I would like to clear some messages from one of my folders.
I have set up a rule which will delete the messages as they arrive, but first time around I would like apply the rule to their current destination folder.
At the moment I can only apply a rule to the whole of inbox.
You’ve read it right — “Process entire inbox” only walks the inbox, and there’s no way to point it at another folder yet.
For the one-time clean-up, search does the job: type the same criteria your rule uses, scoped to the folder, e.g. from:newsletter@example.com in:"Old Stuff" (quote the folder name if it has spaces, and use in:"Parent/Child" for nested folders). In the results, press Ctrl+A (Cmd+A on Mac) to select every conversation, then delete or move them in one go with the toolbar. After that, the rule handles new arrivals on its own.
Search syntax reference, including AND/OR/NOT and date terms if you want to narrow it further: Search with advanced, Gmail-style queries — Mailspring Documentation