You cannot download a new .AFC file while any of the meter runs are enabled, or illegal data values will be reported by AFC manager.
First you must disable all meter runs. This can be done either using the AFC manager, or the easier way is through the ladder logic. Once the meter runs are disabled, you may download the new .AFC file. You will then be able to enable the meter runs.
Also note that some newer AFC modules ship with a lockout jumper per Measurement Canada requirements. If installed, the jumper must be removed per the instructions near the beginning of the user manual to reconfigure the module.