"She was no longer Mary---the Mary he had once known/used to know."
Do both phrases mean more or less the same? Or they have different meanings?
In this case, any distinction in meaning is miniscule. But note that used to can be used in other ways, some of which would have more difference. For instance, "I used to X back then" can mean "I would X from time to time back then." There would be a difference between "There was the yard he had mowed once" and "There was the yard he used to mow."