That matches my experience. Changing the "mains" will likely require a sub adjustment regarding placement, volume level, x-over setting, etc. The reverse is also true. I'm taking it slow, avoiding OC behavior and enjoying the process. I think I found the "magic" combination or, at least to my ear, something that's pretty darn close.
It's always a long tedious process, but worth it in the end. What makes it easier is if you can measure (REW is free). It gets you 90% of the way there, then use your ears for final tuning.