Yes. USB Backup works with shared folders. The only difference is, that the content of the shared folders might or might not be distributed on the two disks. (depending on your settings of mergerfs).
I hope others have an answer to this based on practical experience.
I'm back....
So I was able to update to OMV 5 using the method ryecoaaron stated (link for anyone interested).
I ran into a few hiccups with mounting the second HDD, most likely due to my own error. But it is mounted, and successfully created a Filesystem for the HDD.
I have installed the "Union Filesystems" and "mergerfs" plugins. I don't think I need unionfs for what I want to do, and mergerfs should work. I am looking for a sanity check before I go with my desired setup.
Current Setup:
Disk 1: Has all the data, already organized with several folders and files. Has one Shared folder (which is simply the entire disk).
Disk 2: Blank
I want to simply merge the two together, and continue using the already created folder structure.
Using the mergerfs gui I created the following:
Will this setup work, or is there a better way I should do this? I don't want to end up regretting this a few months/years down the road.
Thanks again for the help in advance.