Fat grafting is an excellent tool in improving the appearance of assymetry/contour issues after previous breast surgery. Inverted nipples can be addressed through small incisions near the nipple to increase projection. Fat or a dermal graft can be used as an adjunct to help maintain nipple volume/projection.
If your nipple inverted after the removal of the cysts, then a fat transfer could be helpful to fill in that area. If your nipple was inverted prior, no, the fat transfer would probably not make much change. I would suggest meeting with a board certified plastic surgeon and discussing your options.