Well I found an easy way to pair an Ouya Controller that was not in the mood to pair with my Ouya.
Turn on your Ouya and press the U button until the two middle lights start blinking.
After that immediately restart your Ouya by disconnecting it from the power (I have only one control).
The two middle lights continue blinking.
When the Ouya restarts the controller is paired.
Practical way after many efforts to find a way to pair again.
Didn’t find the cause but I found the outcome.
Hope it helps someone else also like me.
This way refers to classic Ouya with original firmware.
Hope I have explained it in an easy way.