I think it is unlikely:
From a marketing perspective, it would be a big shift for the "3" brand to go from fast sports camera to slow studio camera. Canon already has a marketing name for their high resolution cameras -- adding an "s" behind the model it is based on (1Ds, 5Ds) and I think they will continue to use that for future high resolution cameras.
From an engineering perspective, it would make more sense to put a different (e.g. higher MP and slower) sensor into the R1 platform and call it an R1s if they want to make a flagship high resolution camera. They already engineered the R1 and I am sure it is improved over the R3, might as well make full use of it rather than designing a new R3 Mark II and have to spin up a new manufacturing line for this.
Finally from a historical perspective, the original EOS 3 was a one-and-done camera, so there is precedent of them launching and then retiring a camera (with a "3" model number!) with no successors.
Thus, I think if Canon is going to make a 60-90 MP camera, it would be either an R1s or an R5s, based on either the R1 or the R5 Mark II, with I think an R5s being more likely.