Possibly they were never upgraded. Did you also not have to set Version back to 12?
If so, directions should probably not call for the DROP INDEX unless version needs it.
Code looks that index came in on Version 13. I think job databases upgrade upon use.
Possibly you only ran 2, so only upgraded 2, so the other 4 were left fine as they were.
At what level? The following history makes me think you picked an unusually high level: