The amount of lr you have should more then make up for the bio-ball removal. If you slowly take out 20% of bio-balls each week until fully removed any biological filtration it provided will accumulate in greater quantity within the lr. You can add the lr rubble at anytime.
I have a Magnum 350 pro with two bio-wheels spinning on the main along with the 90 lbs of base/lr in my 55 gal. Every time I get a new fish I remove one of the bio-wheels to the qt tank for bio-filtration. I have never experienced a nh3/no2 spike from doing that and I suspect that the bio-wheel probably has more bacteria on it then the submerged bio-balls in your bak pak.
As far as the CC substrate goes I feel your pain since I also had to deal with CC with my first SW tank 16 years ago. Of course back then it was considered the “norm” and we didn’t know just how much waste built up in it. Vacuuming does help greatly but unfortunately as you know it’s near impossible to get behind the rocks and clean up crews have a heck of a time digging it out of the CC.
With sand you could use worms, snails, and other creatures to keep your sand bed clean. When/if you get brave enough to replace it I would. The CC does also store some of your bacteria so keep that in mind when replacing and also replace in sections to avoid any spikes.
I helped a friend replace hers last year with the 55 gal tank fully stocked with fish/inverts. We did about a one foot section at a time each week removing lr and scooping out the CC along with a vacuum to keep the mess down and replacing with aragonite sand through a 4” PVC tube. Tank took about 12-48 hours to clear each time but her fish/inverts came through just fine.
It took a full month to replace all of it and about an hours worth of time for each foot but her 4” sand bed looks so much better and she has had 0 no3 for the last 8 months
