There are actually simple and very sophisticated solution (available, but need more consideration in applying to ur case):
(1) A friendly reminder in help regarding the consequence of “remove”, that user can still find the deleted note in trash.
(2) The stack might be easier/ready to implement than you think. Build another tag tree (or tag group to ur liking), setup each tag/tag group to represent one document. Whatever notes/versions of note from the same annotated document can be replicated into the revenant group. So a replicant of the complete stack of notes from one single document is located in the same place and tagged for quick reference. Kind of similar to what the OP on a bookend script does BUT this one is in manual mode.
There is an automatic solution in which @korm said it’s the best he has ever seen in DT forum Make an Annotation with Links, Notes, Tags v2 and Annotation Pane (Annotation with Links, Notes, Tags v3).
(1) The concept of this solution can definitely apply to your idea/s - if not more. But it will take a bit of time to understand the versatility of these two script packages. The solution can even be used in basic qualitative analysis (for those DT users who are not fear of experimenting with scripting).
(2) IMHO: the script v2 has more flexibility than v3 in allowing users to shape/modify its original intended purpose (I am referring to the version of the above-mentioned script, not DT!).
(3) Given the latest features update and the enrichment of AppleScript library of DT3, I can see that there are many room for modification of V2/V3 of this script to tailor for some specific/advance usage (although probably less for my purpose).
Just my 5 cents