as long as you have the extension installed, everything you bookmark will be available in the service, regardless of which instance of chrome it came from.
(I also agree with the comment below that it's an edge case for most users, especially Chrome sync users.)
If I edit a URL, stashmarks doesn't reflect the change in the UI, at least when the original is still pending download. Looks like it's actually changed internally.
Also, I can't delete (or edit) a bookmark in stashmarks that I no longer have saved in my browser. Recreating it and deleting that does nothing, even when logged out and then in.
Hope these critiques are helpful.
Clearly, these are all edge cases, and overall your service is impressive.