You could always further refine the size listing but using du on the Index folder. You don't see anything in the finder maybe because the out of control file(s) are hidden from the Finder.
In the end, just nuking the contents of the Index folder and moving on (reinstalling if necessary and GD is broken) might be easiest. Though if the oversized content IS hidden from the Finder, you cannot select all in the Index folder and trash everything, it'll skip the invisible stuff. Just deleting the Index folder will likely break Google Desktop.
It won't mess up your "system", just Google Desktop.
In the end, just nuking the contents of the Index folder and moving on (reinstalling if necessary and GD is broken) might be easiest. Though if the oversized content IS hidden from the Finder, you cannot select all in the Index folder and trash everything, it'll skip the invisible stuff. Just deleting the Index folder will likely break Google Desktop.
It won't mess up your "system", just Google Desktop.