Editor here, I'd say that you can definitely challenge any edits you're not sure about (be polite!). At the end of the day it's your writing. You may find you agree with some of the changes once the editor has explained his/her reasoning. Or you may want to keep the original writing -- that's what "stet" is for! Either way, the editor has the same goal as you, which is to make your writing the possible version of itself. It's really not supposed to be an adversarial process. Now, an in-house editor may have less flexibility in terms of having to adhere to the publication's style guide. But again, they should be happy to explain where that applies & the reason for any changes.