Hi Madhu,
We have faced a similar issue in our project. As the message is already delivered to ECC through PI, there is nothing that could be done from PI. The solution for this was to go for a periodic batch job developed in ECC which will clear the messages from SMQ2.
There was no impact either in ECC or in PI due to this batch job running in regular intervals of time. You can ask the basis team to help you with the batch job.
Thanks,
Divya.