Usually a huge excess of thionyl chloride is used in chlorination reactions. I typically use it as the solvent along with a catalytic drop of DMF.
So yeah, probably some gets consumed making the ammonium chloride salt, but there's plenty left to make acid chloride.
Kirggy, under acidic conditions that methyl chloride reaction doesn't sound very good. It's a very ordinary way to make esters to make the acid chloride, not really isolate it, then dump in a bunch of your desired alcohol.