It says paired or connected in Settings?
If it says connected, are you sure that windows aren't falsely say that this device is connected? Happens all the time to me.
2 ways to check. If it really is connected, if you press a button, the leds stay on flasing. If they turn off after a little, it's not really connected.
If they stay, check in "Control Panel\Hardware and Sound\Devices and Printers" and right click the Joy-Con (R) and click game controller settings. Select the correct and press properties. Press buttons in Joy-Con. Do they show up? No? Drivers problem.
For all these problems the solution, as I said many times in this thread and have in the retry dialog in my app, is simple:
The microsoft bluetooth stack is generally bad in pairing/re-pairing. Just remove the device from settings. Wait for it to disappear from the list. And then pair it again.
EDIT:
You don't have both of them connected by any chance, eh?
It only supports one at a time. If 2 or more are connected, it goes with this order: L > R > Pro