I am catching up on this thread because I've hit upon a similar need to cut-and-paste text that contains links from Note1 to Note2. As I made my way through the thread, I was quite surprised in how complicated it seems.
I'm in the middle of a writing project and admittedly read through the posts quickly ("focus on creating content, not tinkering with the tool", preaches my conscience). Based on a first-pass through the posts, setting up agents/deactivating agents, navigating links in new tabs -- all seems so complex!
If votes are tallied for new features, please count my vote for a "Paste and Preserve Links" option -- perhaps, it can be part of the Edit menu, like "Paste and Match Style".
With regard to the idea that this is rarely encountered, I'm surprised by that too. I run into this problem quite a lot. In fact, it is more often the case that I want to preserve links in $Text.