Can I chlorine shock my system?

[Dalrock]

I have a Bosch Aquastar 250xso LP and I'm installing a uv filter on my rainwater catchment/cistern system. I've had some rust contamination from galvanized pipes so I want to clean out my house pipes and shock them. Is it ok to run chlorinated water through my tankless? A bypass wasn't plumbed and it seems pointless to shock and skip that but I don't want to damage it either........