Is resetting 'Check hybrid system' frequently harmful?

You will need to keep a close eye on battery temperature... A device like this one: Panlong OBD2 Scanner Bluetooth OBDII Diagnostic Tool Car Code Reader Turn Off... | eBay will allow you to use phone apps like Dr. Prius to monitor the temperature. Once it get above 48' Celsius you risk blowing their tops off. Good news is it's likely your battery pack could be repaired inexpensively by replacing the bad module with a used one. There's 20 modules in your pack and probably only one of them that needs to be replaced. In the US, they only cost about $35.

 

Do you even know why the 'check hybrid system' warning is being shown? It does not always mean you need a battery. It can be shown for around two hundred different reasons, which are identified by different trouble codes.

The next time the warning is shown, a suitable scan tool can be used to retrieve the trouble codes. Only then will we even know what kind of issue you are ignoring by clearing the warning.

 

While we can't be certain... It's fairly well known that Prius C packs are undersized and have a bad cell fail earlier than larger packs at end of the year. Once OP gets the ability to study data they'll better understand, but I bet 90% of the time it's just a bad cell / out of balance block.

 

Start by scanning for detailed codes. Not all scanners are created equal, there's a thread somewhere with details on the good cheap ones that work with smartphone apps.

Then check the battery cooling fan under the left rear seat. Clear any fuzz or debris from the blower, the tubes, and the intake grill. You'll need a screwdriver to pop the panel off under the back seat but it is very easy. You'll want a vacuum cleaner to do the cleaning work. There are youtube videos that show the whole procedure.

If that battery is tired and you're trying to stretch it out, you'll want to do everything you can to keep it cool until you can repair it or replace it.

 

I would advise you to first, relax. Follow the advice of those who responded in suggesting you determine what code is causing the alarm, and ignore those that are trying to make you panic. Could be it is a simple solution that won’t cost you much money, if any at all.

 

I was getting CHECK HYBRID SYSTEM, apparently due to a constantly plugged-in ScanGauge II (on the OBD port). Symptoms included brake and skid control warning lights, and work-to-rule brakes. Disconnected the SG, and have no further "hybrid system" problems.

The CHS light can come on for conditions totally unreleated to hybrid battery. Get codes read to be sure.

If you want to check into the hybrid battery condition yourself, DR Prius app is worthwhile. Works well with a Carista BlueTooth dongle on the (aforementioned...) obd port.

 

This is theoretically possible, but is in practice extremely difficult due to the necessity for new firmware to tell the car how to manage the extra battery capacity.