Hi Vivenka. Thanks for jumping in here, I really appreciate it. Answers to your questions are as follows:
Can you share a file and a journal to investigate further? If you mean the Revit file itself, probably not. It is over 500MB in size, not containing CAD and Revit links, and contains intellectual property my boss would not want me to share.
Have you checked your graphics card for compatibility with your Revit versions and updated to latest drivers? The card is a Nvidia P4000. It is not specifically listed as compatible, but it was a Dell suggestion for what is a pretty high powered workstation. Driver is up to date.
Is this issue specific to a model, have you seen this before? Are there always linked Revit files? Does the problem stop if there is no Link? The problem has always existed when we were using the Adobe PDF driver. We haven't had Bluebeam for that long, but we bought it partly in the hope it would solve the problem. To be clear, this occurs with linked CAD in halftone, not linked Revit. We always have linked CAD files, usually civil and landscape at a minimum. Obviously if there is no link, there is no conflict and the linework appears normally.
One wildcard is that the linked civil CAD file has its basepoint a thousand miles away, and this means that their linework (including the line which obscures our linework in the images above) as viewed in Revit is squiggly. I've posted on this forum about that too, but it appears very difficult to fix and the civil engineer refuses to change their basepoint. But this issue is independent of this. A landscape link with no squiggles does the same.

User-specific? have you tried in another user profile? I just tried it on a completely different workstation (with an Autodesk approved graphics card) and the problem persists.
Any windows settings/ version? Win 10, other user is Win7 multiple monitors? yes remote desktop printing? no
Is Acrobat or pdf reader open when printing? No
Have you been able to reproduce this with other pdf printers? Yes, Acrobat Pro produces identical results. Of course there is no "lines merge" setting.
Double check is that your machine is not running out of RAM - this would very significantly affect the performance of printing. No. This is a very capable workstation with 16gb RAM. As I say, the problem persists across workstations in our office.
I also submitted a ticket to Bluebeam yesterday but haven't heard back yet. Thanks again for your help.