You know, if the trans person prefers a gender-neutral pronoun like "they," then they already should have discussed complications such as this one--in advance, just in case. I mean, I discussed pronouns with lots of people when I was pre-transition and when I was in the androgynous-looking zone. I made everything quite clear. And I was working with gender-specific pronouns. Pretty cut and dried.
It seems to me that this trans person might be living in their own little bubble. I know someone who uses gender-neutral pronouns and lives in such a bubble, so maybe I'm projecting a little. Or maybe I'm seeing an uncomfortable truth.
But I do also feel that the (cis?) partner probably should have anticipated this situation as well, and prepared for it. The farther off the binary grid you are, or the less binary you are at the moment, the more you have to prepare for awkward situations. This also goes for partners of trans people. It's just good common sense to be prepared, yes?