Nice I figured it out.
Inside the method, any manipulation done to the item in question should be carefully ensured that any manipulation is referenced in the xmlDom's own object (making a javascript copy of my variable which I will mention later still let the solution work (it did not inhibit it, it still worked))
The item in question was activity. The method manipulated its relationships via SQL (problem as above, with bug of not updating for promise function) and I instead fetched the relationships, called getRelationships, and then specifically did .getItemsByXPath to get the record I wanted to delete. Calling getItemsByXPath on the variable assigned with .getRelationships meant that I was in fact using a pointer to the already existing xmlDom.
From there, when the variable assigned with getItemsByXPath (<copying this one still works too), I was able to do .setAttribute("action", "delete"), .setAttribute("id", id) and then calling variable.apply(). This accomplished two things one: What the SQL already was doing (deleting), and 2: also updating the xmlDom of the Item activity for when I returned it it would reflect the operations done (the records were no longer there at all, hence the item with action=delete completed its performance and now was gone)
