I have found the following workaround:
- use MSFS in Windowed display mode
- when in VR use CTRL + TAB to exit out of VR session
- use World Map to load or save flight files
- use CTRL + TAB to enter VR session again
It is relative easy to do and I can live with it for now. I did file a request at MSFS zendesk and hope they will make the flight files accessible from within VR session.