Perhaps it was because at the birth of the Hong Li Federation, the Holy Spring had worn out and could not serve as the root source of power. After decades, if not the hundreds of years of renewal, the Holy Spring gradually restored its vitality, allowing the Black Mechanism to re-emerge.
This is also the reason why the Black Mechanism of the Federation borrowed the name of that extraordinary organization from the Imperial Period; they originated from the same source of power.
Besides, Casio made another discovery. He had dealt with the Black Mechanism in two different stages spanning a gap of fifty years.
By observing the abilities of regular officers of the Black Mechanism, one could conclude,
The Holy Spring Water which they used was scarce and weak. At least the quantities weren't really ample, possibly only being supplied to a part of the personnel.