Although dilithium isn't technically the "fuel" (deuterium and anti-deuterium are), it is so critical to producing usable power, that due to the fact that it crystalizes in use means it eventually "runs out" (stops being able to regulate the matter/anti-matter reaction).
In Star Trek IV: The Voyage HomeStar Trek IV: The Voyage Home, Scotty and Spock find a way to re-crystalize dilithium, by the 24th century this could be achieved while it was still in the dilithium chamber.
In light of this, the limits of replenishment have moved to mainly to anti-deuterium reserves.