¿Cómo dices esto en Inglés (UK)? —— Hey guys! what’s the difference between “how long were you together” and “how long did you stay together” can I use these sentences interchangeably? many thanks!

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They are interchangeable, usually. But depending on the situation you might want to choose one or the other.

A: Back then I was still married to my wife.
B: How long did you stay together?
A: Until she died!

(So, it can sound insensitive, if B knew A had lost his wife. "How long were you together" is a safer choice.)

Also, you can't really ask a question like, "How long did you stay together before you had children?" (It sounds like there's a direct connection between staying together and making children.) It should be "How long were you together before you had children?" (or "How long had you been together before you had children?").