So I told my Manager that I’d like to quit work to pursue my master’s & he asked if I had given my GRE. I panicked and told him I hadn’t, as most universities waived GRE. Now I need a professional recommendation letter from him. Is there any chance he’d know my GRE score or that I took the test?
I'm not sure under what circumstances they'd be able to find out, but this seems like a moot point because you really should* just tell them the truth. You made a mistake here and it will probably do you well to correct it. It is, after all, very minor and easily fixable. On the other hand, keeping this secret seems petty and unprofessional, at best.
(Not to mention that it's easy to imagine a scenario where they don't find out, but that still becomes your problem. For instance, what if they view your lack of GRE scores as a serious problem and they spend a substantial part of their letter talking about how capable you are "despite your lack of GRE test"? How do you think that would look to the admissions committee?)
There's no need to overshare or be overly apologetic. Mistakes happen. Just say something simple like "I think I told you that I had not taken my GRE. Actually I have; it just wasn't on my mind since so many schools had waived the requirement."
(* Obviously I don't know your full situation and yes, there are corner cases where this will be bad advice. But I can't imagine a situation where this is bad advice and it's a good idea to get a LoR from this person.)