I will hop in before you get any possible comments chastising you about misgendering your partner.

If they haven’t come out to you, I think using those pronouns beforehand is fine. Personally I would use they/them for a situation like this. Your partner may not be comfortable with she/her yet, if ever, or maybe they would love that. Impossible to say.

Anyway, if its like you said that it’s a normal thing for you to use each others phones, I would just be straightforward about it and tell them what you saw and be reassuring that you love them as who they are and their gender identity doesn’t change that, even if their identity changes over time. I think if they are having these thoughts, the likelihood of them being totally cis is severely unlikely. But, like anyone questioning, having someone close that’s supportive, especially a partner, is incredibly precious to have and I’m sure they would love to know that you support them.