I haven't seen her in a long time.

Literal

[topic-は] long-time [humble-お]meet-do-[ongoing-てい]ません.

お会いしてません uses the humble form お会いする (humble of 会う, 'to meet') in the negative progressive ~していません. This is humble speech (謙譲語) — the speaker lowers their own action of meeting. The sentence is about the speaker, not about 彼女: 'I haven't met/seen her.' The politeness level makes this appropriate for speaking to a third party about someone the speaker respects.