"In the context of this episode, it is specifically to "undrain" (I know it isn't a real word
) the drained crystals. In other words, Kirk wanted the crystal power back to full power and that meant adding power back into the crystals.
MASTERS: Whatever that phenomenon was, it drained almost all of our crystals completely. It could mean trouble.
KIRK: You have a talent for understatement, Lieutenant. Without full crystal power, our orbit will begin to decay in ten hours. Re-amplify immediately."
I think there's some confusion between "power" and "capability" that has to be blamed on "drain" ("deterioration" would have been better). If the crystals simply needed to be recharged, then why didn't Kirk say so
as every viewer back then would have perfectly understood.
If I understand correctly a practical use of crystals in real life is amplification and it appears the dilithium crystals had lost some of this capability. Though I don't see how this capability can be restored by "re-amplification" (a colloquialism, obviously) it probably works very well (like the infamous Heisenberg compensators
"Re-amplification" suggests a restoration of original properties / capabilities of the crystals opposite to "re-energise" or "recharge", IMHO.