I’ve not had this issue before - it might be related to using Stage Manager (which I don’t usually use, I’m exploring reducing my screen clutter) on multiple monitors.
I hook a link to a Bookends entry, and then click on Tinderbox on my (Sidecar) screen. When I invoke Hookmark to paste the link to a selected note, it brings up the selected note in a different Tinderbox file (which is also open, but not displayed or focussed).
This has never been a problem when I’ve not used Stage Manager (I’ve just flipped Stage Manager off, and it works as expected and target the correct Tinderbox document, so it’s clearly a Stage Manager-related issue)
(And I’ve just noticed that Hookmark picked the wrong Safari tab/window with Stage Manager on, so it’s perhaps a more pervasive issue that doesn’t just affect Tinderbox integration)
Hookmark reports Version 7.0 (6534; Integration v. 404) and macOS is Tahoe (26.3)