I would cut back into virgin soil vs. push dirt into the hole. Pushing in means trying to compact what you push into the hole. With only a dozer and excavator, that will be impossible.
As for digging deeper holes, talk with TJ first, I don't know how it's work with the SoilFloc. Think of a bathtub. The plug is either in or out. In and the water level stays the same. Out and, well, you get the gist of it.