I recently had a problem when exporting a project to PDF. In the app full-screen viewer, the links all behaved correctly. However, when I exported to project to PDF, one particular couple of links kept linking to the wrong mockup. These were both on the same page, and were both supposed to link to the same mockup. However, they both linked to the same wrong mockup instead.
I did a lot of testing to try to isolate the problem. I was going to save a stripped-down version of the project to send to you for analysis, but in the process of doing this I found that the issue was somehow being caused by alternatives. When I stripped all unwanted alternatives out of the project, suddenly the problematic PDF links started working correctly.
So, I can’t give you any more precise information yet, but I think you need to take a close look at how PDF exported links and alternatives are interacting. This may well be a confounding factor connected to an earlier bug I raised with groups and links (again, this problem only surfaces in the exported PDF - not in the app itself)