Having tested this I can now replicate it. Steps to replicate
1) Open FG Classic and open two modules
2) Open a map from module 1 and story entries from module 2
3) Drag a couple of stories into the map and create pins
4) Save the campaign and then copy the moduldb.xml file from Classic and add it to a campaign in Unity
5) Load Unity and open both modules then open the map that you pinned. The map is blank (and I saw no pins)
As far as I can see the pin data is all correct in the moduledb file but the file does not contain all of the other information (of course) that Unity requires such as the layers info. Reverting changes in Unity brings the map back but of course removes the pin data.
So it looks like moduledb files are not 'forward compatible' at the moment. I have actually seen this as part of the problem of importing Classic campaigns into Unity. All sorts of image issues are apparent if the moduledb file is not first deleted once copied over into Unity.