That doesn't even make sense. I don't see how permissions or ACL's would have done that. Permissions are just that, they don't randomly delete files.
What exactly did you do?
As said in the original post, I updated the privileges and ACL on the shared folder, it gave me some weird error after trying to apply the changes (mount already mounted?). I just rebooted the vm from inside the shell, since I did not want to waste time troubleshooting this issue. Already weird enough I was not able to update privileges... I did not operate in no other aspect with the system or web-GUI.
I am the only user, that share is only mounted on my Windows machine. I have been using OMV since 3 years, I am running a homelab and I consider myself an advanced user. You can not delete a shared folder if it is somewhere referenced, in my case SMB/CIFS.
In the graph you can see how fast the data disappeared, it is impossible it happened through Windows because over the network this big amount of files would cause Windows to crash/or take longer.
My other 4 shared folders (3 on the same disk) are all in tact.
Judging by the graph the data was deleted before my reboot, which makes it even weirder.