If you create a hotkey from an item in your inventory, then add that item to a keyring, it will delete hotkeys on the first hotkey page (in the same hotkey#). The hotkeys will appear to be functional still (navy blue), but after logging they will appear broken (red) and the same keys on page1 will be missing. I just moved a bunch of familiars that were hotkey'd from inventory items to my Familiar Keyring. I then noticed that the associated hotkeys (1,3,5,11,12) on hotbar-1 were missing. Only the first page of hotbar-1 was affected, the same 1,3,5,11,12 keys on other pages of hotbar-1 were fine (apart from the pages that had the, now broken, familiar hotkeys). I've noticed this behavior in the past, but only 1 hotkey at a time and never made the connection. Anyways, I'm pretty sure this can happen to any hotkey created from an inventory item and then moved to a keyring (familiar/mount/teleport/etc). [EDIT: I don't know how to edit the title, but I'd like to change "Bars" to "Pages").
Yep, that's the one, thanks! I searched for Keyring but missed it... probably in my excitement over finally discovering why hotkeys would sometimes disappear.