ItemsAdder immediately overwrites it on the next /iazip, rendering our work useless.
Well it's normal, how it's supposed to apply changes without touching the zip file?
ItemsAdder (and any other plugin in the world) cannot edit the zip file without, well, editing it.
We're using external tools in order to compress our resource pack
I don't know which tool are you using nor how you trigger the tool, but I can code an event in ItemsAdder API which is triggered when the resourcepack is ready so you can hook into it and trigger your tool to handle the zip file re-compression and optimization.
Would that work for you?
Or you can still continue doing it manually after each /iazip, as I highly doubt you need to make changes to your resourcepack everyday or more than 3 times a month.
Note: you don't need to run your compression tool each time you edit the ItemsAdder resourcepack, do it only when you are ready to release it to the public and you finished your changes. It's not useful to do that each time you add an item when you're still working on the pack updates (my opinion based on how server usually are handled).
I hope this is enough to clarify the situation, have a nice week 😄