Hi Eric, I am sorry to jump in but I am having the same issue, or at least it is related.
My library is composed by files stored on a share in a RAID (synology 412+) plus a directory on external drive connected to the NAS via USB. Many times Roon reports the share on the NAS is not present, however the external drive -that is also connected to the same NAS- remains active and fully available on Roon, which is weird. The only way to restore to normal is by restarting RoonServer.
Last time it happened, even though I restarted RoonServer, I had to remove and reconnect the share (but not the USB, which persisted) and Roon started rescanning my whole library (it´s been two days and still going). Please your help.