I see, thank you for the visual clarification of the problem. I'll see about including this fix in the next update.
I think it's fine to copy individual lines, of course; the problem comes in when pasting arrow heads to other boards. That's just not the way it's supposed to work, and opens up issues due to the way MasterPlan is designed. Lines that span multiple boards could be a very useful and cool idea, but I'd have to re-design some things to get them to work properly.