The MTA is not going to give a yard a mixed fleet if they don't have to. The 6 is most likely to recieve the R62As from the 7 because the R62As are already set up with modifications for 6 service, and the R62As from the 7 are similar in quantity to the R142As on the 6, so there can be a 1 for 1 swap. R62s have no problems running around loops, so I have no idea why anyone would think that is a problem. There would still be some R142As assigned to the 6, but that shouldn't be a problem.
NO R142s have CBTC installed, so it shouldnt matter what group cars they send out. That said, I would expect them to either go from the top down, or lowest number up, when converting R142s to R188s.