Last week I connected my scan tool to my 2007 Prius and read/reset DTCs regarding the HV battery. I actually did it a couple of times. Then I took it to the dealer and they said I needed $3800+ work including a $3200. hv batt. I had a hard time dealing with $176. to replace spark plugs so I did it myself in less than 30 min for $28. - $8. rebate. (Just remember to reconnect the right spark plug connector, DUH!!) And $231. for an OEM 12v batt. so I got an Yellow top Optima for $175. Everything checks out fine. Now they get their money's worth with "If it fits, it ships". 2 days across country. Anyway, I reconnect the scan tool and it tells me the motor isn't running when it isn't -- good! But when I start it it says it can't communicate with the scan tool. Moving right over to my Honda Van, I have no problem connecting to it. BTW, I tried this before and after replacing the 12v batt and plugs -- same thing. What changed? Something the dealer did???
Have you checked the fuse for the OBD2 connector? In most vehicles, its shared with the 12v auxillary (cig lighter) outlet but Im not sure on the Prius.
What tool are you using? Is it possible there's some protocol differences between your Honda and Prius? Did connecting it to the Honda put it into a certain mode that needs to be changed back?