Ah that would definitely do it I think! Because Dendron will think the note is already deleted (since the deleted note had the same ID).
This should be something Dendron handles gracefully though. I think the easiest way to handle this would be to show a warning when the note is added that the ID is a duplicate.
I'm not sure that this is the same issue as the one Soto Ducani filed, although it may be related. Would you mind sending a bug report as well, or at least commenting on that issue to add this?