I have been runing into this issue with inspector footnotes sometimes disappearing. It has something to do with copy and paste. It always happens when am editing out "(linked footnote)"s. I would copy the footnote inside the inspector, delete the (linked footnote), create a new inspector footnote in shift-f5, paste into the newly created footnote. Thefootnote stays, but sometimes if I switch windows, or edit some other part of the text, the footnote mysteriously goes blank and I have to go back many steps to undo.
Is this also related to the “convert to default formatting” but as well?
If you go to Help > About Scrivener, are you running version 1.7.3? We fixed a bug in 1.7.2 that could prevent the note from saving correctly after the paste when it wasn’t edited further. That seemed to clear up the issue for the users who had originally reported it, and our testing, so if you’re still seeing this in 1.7.3, we’ll need to try to track down more specific settings that are causing the problem in this case.
The conversion issue is related in that it has to do with when the save is (or isn’t) triggered for the linked notes. They’re not exactly the same bug, though, with the same solution. Ironically, the fix for the footnote problem between 1.7.2 and 1.7.3 may actually have upset the conversion saving, as I believe that had been working. This one is on our list, though, and simple enough to replicate. If the footnotes are still not saving properly in 1.7.3, that we’ll need to investigate.