Well, it definitely has to do with typedefs, although occasionally the error is about a VI, but it is somehow connected to a typedef, usually an enum. and when I fixed that error by making some changes to the enum, save and then undo those changes, the error would happen again with a different typedef.
But I had to move my workplace and setup everything in a different place and low and behold, it simply worked after that and has kept working!
The only difference I can think off is that I'm here connected to the internet through Wifi, while in the other place I had a docking station through USB-C. However the deployment does not go over this connection, that is connected directly to a built-in ethernet board on the PC, configured with static IP.