I think that pulling the bio-balls would be fine. If you have been using them for a while I would remove 20 - 25% at a time so your biological filtration will catch up. A 3" sandbed is not quite deep enough to establish an effective anerobic zone. I would increase the depth to >4". I might go with
LR in the A chamber because I think the inflow would crater the sand, possibly even deep enough to affect the anerobic zone. I would not use small
LR rubble but bigger chunks so they trap a minimum of
detritus. The rock will need to be completely submerged or it will just work like bio-balls.
