One fun idea on how TOS dilithium might get "reamplified" or "reenergized":
Note how unlike the paddles of "Alternative Factor" are from the crystal lumps of "Mudd's Women" and "Elaan of Troyius"? Perhaps dilithium in the TOS era is so rare that the lumps are virtually never available, or tend to be so full of faults that only small parts of them serve any practical purpose. So for the most part, Starfleet uses arrays of very small dilithium shards or microcrystals, embedded in those ping-pong paddles; the arrays need to be aligned in a specific way to best mimic the effect of a single, paddle-sized crystal. Yet the microcrystals easily lose their alignment, and energy has to be inserted to restore it, lest the amplifying function of the array alignment be lost and a mere useless collection of dilithium shards be left.
A natural crystal behaves differently: you don't get much effect on one of those with an energizer, but you can tilt a natural crystal to find a good, unused facet. It's a demanding process even for Scotty, as shown by "Elaan", but it can be done. It's still demanding in TNG "Skin of Evil", but by that time, in situ recrystallizing can correct the faults that develop in a natural crystal, reducing the need for facet adjustment and prolonging the life of a crystal.
With the main energizer out in ST2, Spock's only option would be to find a good facet out of the strained dilithium in the reactor; he'd access it via a dumbwaiter system similar to the TOS one, manually tilt it to the required position, and reinsert...