My house is being re-piped by replacing all of the copper with PEX starting at the water service entrance. I'm on a well which is 150' from the house and the service line is CPVC. Currently, there is a ground connected to the copper cold water side of the water heater which connects to the neutral side of the main electrical service panel. There is also a ground to a grounding rod at the service panel.
My question is what to do with the ground connected to the copper at the water heater? I'm assuming it is only there to bond the copper in the house for safety and since all of the copper is being replaced with PEX it is no longer required. The copper wasn't being used as a second ground because the water service to the house has always been plastic to the foundation.
In your main electrical panel there should be a ground wire connecting to the ground rod. If there is another ground wire connecting to the homes plumbing (or from the ground rod to the plumbing), the main electrical service is using your homes metal plumbing as a second ground. Even if the service line is plastic, the metal pipes may be an effective ground if some of them are in contact with earth or a concrete foundation. Thus if you are removing some of the original ground system of the home, you may need to add an additional ground rod. It's a good idea nonetheless. New code specifies 1 ground rod measuring less than 25 ohms or 2 ground rods >6ft apart regardless of the measurement. Since the measurement itself is difficult most electricians just put in two.
There should be a ground conductor running from the main panel to the water heater and connected to the water heater at the terminal block of the water heater. If there's not, add one. If the branch circuit for the water heater is run in metal conduit, the conduit itself is the ground and should be connected to the water heater according to the manual of the water heater.