Sorry to revamp this thread but since it seems not fixed yet, I think it could be useful to share my experience too.
I've had the exact same problem since a while.
My HW is an old desktop PC.
The OMV is installed on a small SSD while my shared folders are located on two mechanical 3.5 hdds.
The HW is perfect, the disks are in good condition, I have no power issue.
To solve the problem I replaced the internal SATA connection cables with new ones, I tried to switch various SATA ports, deep analyzed the two disks. Regardless of my attempts with every power on, the shares on one of the disks are not visible on my DLNA client.
If I try to rescan from the web interface the effect is unpredictable: as a result I can see all the shares, or the same shares as before, or the shares from the other disk. It's crazy, there seems to be a random bug.
One important thing that Mike Warren probably can confirm is that I never have this problem with any version of OMV 5. The issue has started with OMV 6.
My two cents: this kind of issue sounds like a sort of race condition.