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Only one file is needed fr the pdf, the other is in a different folder.
Admittedly it was an unwise thing to do, but it happens.
I just tested this with FrameMaker 2019.0.6.956. Everything worked correctly.
What I did:
Book with two FrameMaker files, one of them in another folder on the same drive.
(I tested this also with only one of the files in the book.)
Both files open.
Created PDF. No problem.
Is this your setup? Can you describe your issue in more detail? Do you have this issue also with other files?
Are your files unstructured?
What's your FrameMaker version? Can you update it with Help | Updates?