It seems you are facing similar issue what we have faced 3-4 times. So far we still not have root cause of this issue but we solved it by recreating sub-interface again. You may try it in maintenance window.
Also there is small confusion:
From PE2 to PE1
3>Ping to PE2 subinterfaces belonging to VRF ,observed drops.(ping vrf cmd) >>> does it mean self-ip is also showing drops?
4>ping to loopback ip using ping mpls PE2_loopback_ip, observed drops.(this is happening in normal hrs also) >>> this looks bit strange. Can you confirm it again.
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