No, he knew she left and watched her leave. My issue with it was just handled in like a page of flashback. The not telling Clark thing was incredibly dumb and really served no point. I think the idea that Lois would find herself a little out of place and unnecessary with Jon and Jor El on their trip isn't ridiculous - and the idea that she would be a little overwhelmed with being treated as royalty off Earth could have worked really well into Clark going public and her issues with her own dad - but it all just kind of happened to happen to get pieces in place for another plot point as quickly as possible. And her having friction and being a little ansy to get back to work worked well as a subtle dig to the pie baking Rebirth Lois, but again, it wasn't executed well and could have been handled much much better.
For all the flack Bendis gets for decompression, I found his whole run to be incredible rushed. A lot of it reads like outlines. I think he'd be better served at this point as being like a "showrunner" for the books and then other writers were able to flesh out his ideas.