I don't think that meant that they hadn't seen each other since he was cleared. He's just been cleared as being well enough to come back to work. So when she said she hadn't gotten the chance to tell him how glad she was that he was okay and that he was back, it was in the context of work - she was glad he was medically okay to come back, and hadn't had the chance to tell him that day because they'd been busy with the case. She hadn't had a moment alone with him since he'd gone to the hospital for his final check-up. And to me, she only looked sorrowful when Eric was despondent over what was happening to Ethan. I don't think a verbal response from him was necessary, especially after he told her "you always did read me so well". I think the look on his face when she asked him totally said "I think you know the answer to that question, silly woman". And he did follow up her statement about CSI not being the only game in town with "Like I said, you know me so well". Just the look on his face & in his eyes was enough, she could read that - of course they were still "you and I". To me, the lack of a response was completely okay given the message that she knows him so well, better than anyone else there, including Horatio. CSI not being the only game in town simply mean that being a CSI isn't the only thing Eric can do (for a job) in Miami. There is so much more he can do as well. Like being a reef tour guide with his own boat (like in Speckles' story). I think she cried because she was going to miss having him around at work. I mean, they met and really got to know each other there, and have worked side by side for more than 8 years, so yeah, I think she'd be sad enough to cry when he leaves the job. She won't have him around her during the work day anymore. I'd be sad too! She cried when Alexx left, doesn't it stand to reason that she'd cry when Eric left work? She still sees Alexx, and she'll still see Eric - but not having them around at work was sad for her.