It sounds like you want to do a wet repair. If so, the only material that I have used that I'm sure is safe is one of the non-toxic marine epoxies sold to cement coral fragments.
I have used very small amounts of silicon sealent wet with no ill effect, but I have never used more than would be needed to patch a small hole.
I assume that everyone knows this, but becareful to only use aquarium grade silicon. The fungicide added to ordinary silicon sealent will kill stomatopod and octopus.
Roy