I agree wirh Kyle. The patterns are stored as a digital program whereas the transportet is a more analogue dvice. The term matter to energy could refer from energy being used to assemble the atom (wheather the replicatirs have a bank of elements they used to build or build the atom at of pure energy), this is pure guesswork, but is the only science bases stragey that may work based on the level of technology they have. This could explain why latium cant be replicated, due to a quatum signature which the atom builders cant produce. However, theroticaly replciaors could work off the princles of quatum supersition, everything exiting in every palce at once, and you merly control that.