Hi Deepak,
It is possible to run two instances of S32 Design Studio under Window environment.
The limitation is you cannot open the same workspace twice. Therefore for the second instance of S32DS must open a different workspace with project you want to works with.
If you intend to debug both project at the same time you should also adjust GDB server ports + select a different P&E Interface instance.
e.g. one instance uses default GDBMI + Server port and the second instance uses 6324, 7324 ports (if these are not use by another program)
Hope it helps.
Stan