I'm having the same issue on my Client provided laptop (I'm a consultant). One of my folder portals always disappears. However, I noticed if I mapped my portal to a subfolder in that same directory, it would stick. After it held, I tried re-mapping it to the parent folder, but then it disappeared again.
I wonder if it has to do with the folder name? This folder name that keeps disappearing has Square Brackets in it " [External Access] ". My client uses that to indicate that their outside clients/customers have access to the SharePoint site. However, I have another one with Square Brackets in the name that sticks.
Also, I map to another folder with a very similar name but no Square Brackets, which is the internal site for that same project. That one stays put, not like the External Access one.
Both folders start with "Project Name - ". Not sure if that is causing some sort of glitch for either OneDrive/SharePoint or Fences or the interaction of the two.
I did think it might be related to the "On Demand" feature of OneDrive/SharePoint, so I created a text file in the top level of the folder I wanted to map to that I used as an "Anchor" and changed the settings to "Always keep on this Device" for that file, but that didn't help.
One other data point, as I said, I'm a consultant, so I also have this mapped on my Consulting Laptop. It works fine there. Both are running the same version of Fences, but I did notice that the OneDrive versions are different.
Obviously, the client laptop also sits on their domain and has lots of other controls and policies in place from IT. Maybe one of those settings is causing this issue.
So, to recap. Having the same issue that others are seeing, but only on one of two laptops. Same mapping and to same folder works on one but not on the other. Hope that helps someone figure it out.