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Had an interview with two (only) partners at a small firm together. I would like to send them a thank you letter and was wondering if it is acceptable to email them one collective email Dear X and Y: Thank you for...

I met them together so if I sent two separate emails they would probably talk to each other about it noting it said the same thing.

They likely won't talk about your email at all. But, in any case, Send separate emails because although you met them together, it's more personal to send individual emails and they might like that better than being lumped together. Try to personalize each email to something specific that you talked about with each person.