Usually a software upgrade on the 6509 is relatively painless, but this time it proved to be very painful. The previous software load on the VSS pair was 12.2(33)SXI, but it was the modular version (keep this in mind it's important). The new software load suggested by TAC was 12.2(33)SXJ1 which as of SXJ is only offered in monolithic versions.
Assuming that all was well with these two versions, I started down the path of doing an enhanced Fast Software Upgrade (eFSU) of my VSS pair using the ISSU commands as listed in the Catalyst 6500 Release 12.2SX Software Configuration Guide - Virtual Switching Systems (VSS) on Cisco's website. After issuing issue loadversion disk0:s72033-ipservicesk9_wan-mz.122-33.SXJ1.bin on the active console, I waited for the standby chassis to reload. Unfortunately it entered a reboot loop because the new software was not compatible for ISSU. Here is where it got hairy. At this point I could neither abort nor complete the upgrade on the active supervisor. It wouldn't let me change the boot system variable because it had a state somewhere that said it was in an ISSU upgrade even after power cycling the chassis.
After 5 hours on the phone with TAC, we were able to clear this persistence and finish the upgrade, but it was a very long downtime. The moral of the story... modular and monolithic IOS don't mix well.