I came across a thread a day or so ago on one of the sub forums on this very same topic but was not able to find it for you. There is such a range of responses to physical strains that even experts have difficulty sorting it out. My knees generally behave but just the other night, out of the blue, one knee woke me up due to discomfort, then the following day the issue disappeared. No known reason.

My suggestion is to search for that thread which linked to an article listing many issues relating to cycling pain with possible caused and cures. For example, some cyclists need a different Q factor which may be resolved by moving the cleats on shoes or a wedge under the cleat or orthotic foot beds. An immediate thing to try is to go back to platform pedals temporarily and if that helps figure out why. Good luck