My first question is-are you gonna run 9 frames? If not pull the spacers. If you're gonna use them-I'm thinking that the easiest way to get rid of the propolis would be to pull them off the boxes, torch them with your propane torch, and re-install them.
I would remove the spacers and scrape the propolis with a hive tool. You don't want to start a box of foundation with 9 frames. You start with 10, then remove one and space out 9 if you want to run 9 frame boxes. Starting with 9 frames of foundation, or foundationless, will give you a cross comb nightmare.