A follow up post with the issue and solution in case anyone runs into this in the future.

Brett @ RTi worked with me to figure this out.
Apparently the failed wifi sync caused the incomplete program to be stuck in memory. Any program I tried to download was added (size-wize) on top of the failed one and caused the memory to fill up.

Reboots, Re-sync and even new firmware didn't get rid of the incomplete program. Brett pointed me to a flash eraser that completely wipes the memory. Very similar to flashing the firmware. This did the trick. Once wiped, I could again load my file.

Needless to say, I will be syncing over usb on the T3vs from now on. Lesson learned.