It has to work in context. In a modern, US context, "whilst" usually sounds stilted or pretentious. Editors are right to flag it. As for "fortnight", it's a little used term in modern language, but not one superseded by an alternative. If it fits into the context, there's no reason to shun it.
Whilst I understand the argument, I fear I don't understand the dilemma. Using whilst is up to the writer and could be totally content dependent, for instance if you are writing historical/period pieces that may contain conversations that define a particular character. I happen to adore the word and I've read many published pieces where it was used and I'm from the east coast and intend to publish in the USA - using 'whilst'... Hope you don't mind me making my virgin post here Hello!!
