Let me explain what I did. When I first started playing with the various nav programs, I also made the "necessary" sys.txt entries so as to share content. As a result I started also to get that error message. What I did was to put all the navs on one SD card with the content being separate for each program and added the sys.txt entry to Primo:
has_secondary_root=0 so I could have all of them on that one card. Unless there is a space issue this is what I would recommend you doing. You also might want to limit the number of maps you need to what you actually use.