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Re: "the way in which " is this section any problem?

You haven't provided a full sentence or any context, so I don't know why you think it is ungrammatical.

Certainly, examples like these are impeccable:

I admired the way in which she handled the situation.
I'm appalled by the way in which you spoke to him.

In both those examples "in which" can be omitted altogether or replaced by "that". But they are not better or more grammatically correct alternatives -- just different constructions that have the same meaning.