Michael didn't mean it literally when he talked about 'starting from scratch.' Unfortunately, the reality looked different. He was forced to cut a lot more out of Alice than expected. He removed the two biggest spots of Blood Incursion on her Soul and infused two 7-Star Soultrait Symbols before working on the small and mid-sized Blood Incursion spots.
At first, it looked like Michael would be done quickly, but it didn't take long for him to realize that the Blood Incursion spread much more through Alice's soul than expected. Michael was forced to infuse more SoulStar Fragments into her than initially expected. It was good that Michael didn't invest too many SoulStar Fragments into the Untamed Awakened and the Nest…or himself. If he had gone wild as he would usually to upgrade his Soultraits, Michael wouldn't have had enough to mend Alice.