I've been continuing to receive the "topic X was archived or removed" notification for edits like this page blanking. These edits happen all the time, and they're generally quickly reverted, but they're a lot more annoying when they now generate notifications. Notifications from them are nearly as frequent as notifications from actual archiving, so this is a significant issue that I really hope you all prioritize resolving before DiscussionTools leaves beta, @ESanders (WMF)/@PPelberg (WMF).
My suggested approach would be that, for any edit that has the "Possible Vandalism" tag (like in the example) — or perhaps any removal at all that's a blanking, or that's made by a human editor rather than a bot — you build in a delay (say, 24hr), and only send the notification if the edit is not reverted after that period. This would substantially reduce the number of spam notifications. I also see little downside risk for legitimate removals — by definition, a topic being archived has become stale, so a slight delay in the notification is unlikely to be an issue.