However, he does not replicate an entirely new brain stem, does he?
He replicates entirely new neural tissue. Whether this represents 5% of the brain stem, or 95%... Why should it matter?
I also should point out that not all uses of the word "replicate" should be understood as "used a replicator." The word has its own meaning.
It's quite noteworthy that in the one ambiguous case, that of "Ethics", the process of replication still consists of making something out of nothing in front of the eyes of the audience, while having the thing glimmer and sparkle. "Replication" in Trek seems to mean one and the same thing even when we might expect it not to.
That doesn't necessarily mean that even the food replicator should be utilizing only one type of process or gizmo. Quite possibly, there's a whole factory inside, with multiple fascinating techniques in use, and with just the end product finally materializing via the help of basic transporter technology.