Before I installed a NAS I used NFS Manager on Mac. This was in the days of Yosemite & El Capitan. In order to use NFS reliably, I had to turn off Samba in the Advanced Options of the Sharing preference pane. I haven't gone from High Sierra to Mojave yet but I'd assume that option is still there. Unless you need Windows file sharing for other purposes, you might try making sure that's off.
I also needed to make sure that Samba was turned off in the Med, but you've likely already done that. You might try alternating between TCP and UDP in the NFS Options to see if that makes a difference.
I wasn't sure from what you said whether you do or don't have an updated NFS Manager. Whatever version you reinstalled, I do remember that I had to define NFS shares within the app. Perhaps deleting those shares and redefining them could result in proper functioning.
It could be that I'm being no help to you so far, but what I would do after trying everything NFS-related is try using just Samba sharing in both the Mac and Med in order to see if the folders repopulate.
Not having Mojave, I can't test further to make suggestions, but the possibility does exist that Mojave simply screwed up NFS sharing. Also, every subsequent Mac OS seems to relegate to the abandonment pile (or cripple in one way or another) more and more apps that aren't yet 64-bit. Marcel Bresink might have more insight than is what is contained on that support page.
The last possibility is, as he stated there, the NFS protocol in the Mede8er is just too old to function properly within the new Mojave OS. I've had a problem properly logging into the shares on my NAS with NFS since updating the QNAP NAS OS. I've suspected a permissions issue but can't find anything awry, and I've also wondered if its implementation of NFS was just too new for the Med.
BTW, if you didn't know, there will be no more Mede8er updates because the units' CPUs are so outdated. Consequently, there's no chance that the NFS protocol can be updated.
I hope something here might help or that you can determine something else that's causing the problem. If you do, please comment back to this. Good luck!