Concrete base problem in garage shop. Any construction folks?

If the original floor failed, there's a reason for it. Clean rock can be used for significant lifts, but it needs to be contained because it won't pack. When properly contained, it can lock together and be quite stable. But if it's just loose fill over grade, then it can spread and shift and changing the last couple inches of fill may not have much impact if the base continues to shift.
The root cause of failure of the original slab could be many things. If you can figure out the cause, then it will help point you toward a solution.