Hi Vikram,
The messages in holding status are not getting cancelled since the most of the messages are far away from the adapter or integration engine (whichever be the case), they being in queue. The message closest to the adapter / integration engine is preventing the rest of the messages from getting cancelled, since they are far away from the deliverable points. This is obviously due to QoS being EOIO.
Hence the only solution will be if the message are inbound to PI then please request the sending system to stop sending any further messages for the time being. Or else if the messages are outbound from PI then please stop the flow in SAP for the time being. Then temporarily make the QoS as EO (Exactly Once). This will make the messages reach the deliverable points AE or IE. And then you select all the messages and start cancelling these messages in group 
.
Once done, please resume the message flows and change the QoS back to EOIO.
Hope this helps. Reward points if helpful.
Kind Regards,
Souvik