By chance something similar occurred, after removing, turning on, and re-inserting the external SD card (Lux 5 only). This is with firmware 6.7.x
All config settings were reset, and no annotations in the Notes app.
Solving it required switching back to the 'default' profile in the settings menu. So somehow it switched to the card profile for both settings+annotations. Weird.
Also card profiles appear to be hidden in the profile listing.
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