I agree, we should add a feature like this. However we should probably remove the 500 notes bulk suggestion limit first.
The easiest way to bulk suggest all changed notes right now is to just select all notes/cards in a deck and bulk suggest them. (The add-on will filter out unchanged notes and won’t create suggestions for them.)
Alternatively you can use the AnkiHub -> Modified After Sync sidebar item in the Anki browser to first show all notes which are different from their version on the website, and then bulk suggest all of these notes.
If there are more than 500 changed notes, you will have to bulk suggest them in parts at the moment.