Hi Sree,
If the patch was applied but the SAP directory is not there, I guess somebody deleted the directry manually. I was involved in such a case recently. Check and ask your colleagues who has admin authorization on this mashine, if they know what happened.
P.S.: Using the SAP RUNINSTALLER does not make any difference - at least regarding the Upgrade Wrapper patch - as the SAP RUNINSTALLER calls the Oracle runInstaller, nothing else.
Regards,
János