Usually when you dig below the body there is a little bit of slack in the feeder line and you can gently tug to raise the body. This is one of those things the manuals will tell you not to do but everyone does anyway. Then replace the dirt, pack it in, and replace the sod.
If they are too deep or if the head isn’t easy to pull you will need to buy cutoff-style extenders with the correct male & female ends. If you have to unscrew the body you should remove the sprinkler head and flush it out. Of course, with a Rachio you can start and stop the system without walking back to the controller!