its ok to briefly take them out of water, its not that brittle of a biosystem, the natural nitrate reduction biosystem.
those blocks are porous all the way through...denitrifiers abound to the core
brief air exposure isnt going to harm the denitrification.
o2 isn't lethal to that kind of bac anyway, its just not abundant in the strata they've adapted to extract energy from and some presence of oxygen doesn't kill them.
stratification turnover is common at certain zones and the bac simply rebound accordingly.