We handle his by looking for the .stfolder file in the folder root. If this is gone, we will interpret it as a mount failure or similar and stop the sync. If it is still present but other files are gone, we interpret it as an intentional delete. It’s not obvious to me how we would do this better in an automatic, cross platform way - but I’m open to suggestions.
Your setup with encfs is inherently risky from this standpoint, as you’ve noted.