Hello @srikar_26,
Both PTC6 and PTC7 or PTC8 and PTC9 pairs can be assigned to the LPUART 1. However, PTC6 and PTC7 are connected to eh OPENSDA which behaves as a USB to Serial Converter.
When you say that it works on the PTC8 and PTC9, then you are using an external USB2Serial?
The reason for which the PTC6 and PTC7 are not working can be related to multiple causes, like the driver for the OpenSDA, or you are trying to use the FreeMaster at the same time on the same pins.

Waiting for your reply,
Marius