EMC Powerpath showed no SAN disk configuration

What OS are you running ? And I'm curious why you upgraded to PPath 4.6 and not to 5.x, which is newer (and better).

server running on W2K3 R2 SP2. powerpath v4.6 is the "approved" version for our environment.

forgot to mention, there is a SAN disk information showed after ran the INQ.EXE

With 4.x versions I konw there's an issue if you upgrade without first deinstalling any PPath patches. In such a case you'd need to deinstall any PPath patches first and then do an upgrade, but I'm not sure if this is the case with you.
If you didn't "tweak" PowerPath a complete reinstall is always an option. Simply deinstall PPath, reboot and install the new version. Since you didn't change zoning or masking, your LUN's should be visible right away

if inq can see your devices that something is stuck in PowerPath config, search your drive for powermt.custom ...rename it to powermt.custom.bak ..and reboot the box. See if that helps.