It's pretty ambiguous to what degree the citadel can remotely control the relays. I suppose it could remote activate them though some kind of QEC circuit, so it wouldn't matter where they might have drifted off too, but to actually function and transmit the wave, they still need to create the massless tunnel between matching pairs. What if one link in the chain has been destroyed or put beyond the range of it's partner relay? Whole branches of the network could be isolated from the main hub and there's nothing the citadel itself can do to remedy that. I suppose it could direct a relay to move under it's own power (if they're even equipped with that function) but anything less than a full blown FLT drive and nav system and that relay could take *years* to get back into position.