(This is at least true on Windows, but I don't see why this wouldn't also affect other operating systems.)
If auto-profile is currently set to Active, and you use a Default profile for no-match scenarios- you're going to have a bad time with Save As and Load operations. My profile building is iterative, so I often clone profiles over with Save As and work on them for new games. Invoking Save As (or Load) when there's pending changes on a profile makes the no-match scenario invoke- prompting if I want to Save, Discard those changes, or Cancel entirely. This window will end up spawning above the Save As window. This feels like messy UX that could be prevented.
In regard to all AntiMicroX-called OS file selector windows (Save As, Load, any others):
Deactivating auto-profile, editing and saving profiles, reactivating auto-profile. This is how it's always been and isn't ideal. It also seems if I'm willing to take the risk of it misbehaving, hitting Cancel on the window that pops to save pending changes seems to stop the profile-switch from occurring temporarily.
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