CPD are small and get sucked up when removing the sediment.
Unless you made a mess of the sediment and just hate it etc.......I'd just leave it.
You can still add a small amount of ferts to the water column either way.
I'd siphon the sediment out and leave the fish in other wise. I'd not uproot the plants, but also not suck them into the siphon obviously.
you might need to do a few water changes to get it all since this can be slow going, do a 50-60% water change , then refill, then go after the rest of the sediment to be removed.
A few times of this, all of it will be sucked out.
Larger siphon hoses= do not get clogged, smaller ones do.
I'd just rinse the sand real good. Black flourite sand is nicer than onxy IMO.
But it's not any different cost wise as the bags run 15-25$ and you get 1/2 as much as say the ADA AS which runs about 40$, but are 2x the size/volume.
No reason you cannot use both the sediment and the water column also.
Both work and both work together.