I've been doing it for over a year...... Each time i clean out and refill the reactor (about every 6 months) i add a few new colonies up top. Its actually kind of fun getting to watch them dissolve over time.
1. If they are not ground up they may have less surface area than typical media, so may dissolve more slowly.
2. If your tank had elevated levels of metals or phosphate, the skeletons may have incorporated those and so may release them when dissolving.
The main reason they died was due to an alk spike. I dont just use the dead stuff i mix it up like said above. Im also not putting giant chunks in but braking them up into smaller chunks. Thanks everyone for the input