I have Poser 11.3 on the C drive and main factory runtime on an external drive. Just because I like to keep a lot of free space on the C drive.

I have dozens of runtimes with old content, on an external drive. And I have to add them again, each time I update Poser. Even keeping your existing preferences doesn't keep your runtimes attached. At least it doesn't for me. Maybe this is the problem the OP is having?