The notification “has been modified externally, merging changes automatically” pops up every now and then when I’m editing a note. It doesn’t delete anything but my cursor becomes unfocused and I have to click the note again to resume typing.
This is probably related to some plugin that makes changes to the note on the background as you type, for example updates the modification date in frontmatter or something like this. The warning appears if the plugin tries to change the note at the same time as you try to edit the note yourself, because the changes can potentially conflict. You should try to find the plugin that causes the issue. I don’t know if sync can cause it too, but you can try to disable it too to make sure.