Arrrrgh.

Just got back on the computer for the first time since last night and... All the rules I inserted are GONE. WTF.

EDIT: (a little while later....)

More poking reveals a file called SyncedFilesInfo.plist which contains the path to the rules file previously mentioned, the empty signature file and a smartmailboxes file.

This file is a preference telling Mail that each of these is being Synced with iCloud. Something I've never set up and something that explains what's happened.

My guess is that Mail went to sync with iCloud for these items and since nothing is in iCloud it cleared all my local content instead of merging it. I still consider it an egregious bug, but at least I'm confident as to the cause of the issue.

There's also another rules file called UnsyncedRules.plist that I've now copied my rules into. The came into Mail already turned ON, unlike before, and they've survived multiple quit/restarts. My hypothesis is that these will not be blanked because as the filename implies, they're not going to sync with iCloud.

In terms of the larger picture, there is absolutely no option that I've seen to specify that any of this stuff should be or shouldn't be synced. Now any way to control whether or not a newly created rule gets synced or not - the test rule I made did end up in the SYNC file.

Clusterfuck.