The question has two answers, and that's the whole problem
Almost everything written about winter flies fails at the first step: it treats "flies" as one animal. It isn't. The word covers at least two situations with opposite explanations and opposite fixes, and which one you have determines everything.
Cluster flies are outdoor animals that use your house as a hotel. Fruit flies, drain flies, phorid flies and fungus gnats are indoor animals that use your house as a farm. One group is dormant and harmless and cannot reproduce where it's sitting. The other is reproducing right now, in a specific findable place, and will keep doing it in July just as happily as in January.
So the honest answer to "where do flies go in the winter" isn't a destination. It's a question back: are they big and slow at a sunny window, or small and busy around your sink?

