The distance between PH & CH is very walkable. They are opposite to each other diagonally on each end of the same street, may be 1/4 to 1/2 mile apart. CH is almost directly accross from the Tokyo Metropolitan Government Towers.
You can have PH to transfer your luggages to CH when you check out. You then can go do your own thing and later check in CH.
When we were in Tokyo this spring, we stayed at PH first. Then we checked out and went to Osaka. On our return before flying home, we stayed the last night at CH. I asked if PH could transfer our 2 roll-aboards to CH after we checked out. They did it complementary. Upon checking-in CH, the check-in desk immediately acknowledged that. They delivered them to our room in 10 minutes and required us to sign a receipt.