At some point you need to commit and bounce down those plugin saturated tracks. Just my opinion, of course.
You don’t mention any specifics about track types or track counts or plugins used so how is anyone really supposed to give you any suggestions?
I like to create new, clean versions of tracks I’m happy with. Then, I’ll disable the previous version of that track. After making any significant modifications to a project I’ll do a “Back up Project…” (File dropdown) and start a clean project knowing I can always go back and open the old one to retrieve anything, if necessary.
You really need to create a procedure that works and makes sense to you. Everyone’s needs are different. So … care to share any more details?