I have most of my shared stuff on networked storage. If this storage disappears, for example when I update it, fopnu will receive error 67 (ERROR_BAD_NET_NAME) and mark the directory as offline. It would probably make sense to probe this directory every minute, and perform a folder scan if it's available again.

Same problem here.
I suggest it should retry regardless of the type of error received. The error might as well happen because of an unplugged USB harddrive.

Temporary fix: You can create a task in fopnu itself that makes it shut down at midnight, then create a task in windows that runs 5 minutes after midnight to start fopnu.