Best practice for benchmarking involves keeping track of all energy types and meters in order to track overall consumption over time.
When a meter is replaced or retired, it should not be removed from the building’s entry in Portfolio Manager, instead it should be marked as "inactive". Meters that are marked inactive and do not report energy consumption within 12 months of a building’s period ending date are not factored into a building’s ENERGY STAR score.
To mark the meter as inactive, you would use a PUT call to update the inUse and inactiveDate elements for a given meter. An example might look as follows:
<name>Electric Main Meter - INACTIVE</name>