I think your best bet would be to pick a time when the load on the entire system is running normal or average. Then play with moving things around on different branch circuits if possible until the reading near the utility meter is close to what you know it should be. Then just leave it at that. From there it should average out.
Like Melanie said, you can make the utility meter slow or stop or run backwards. In some rare occasions the utility meter will run faster than it should. That is why the system needs to be "balanced". Good electrical contractors on new construction or revamped systems try to do this.
That is why you see them running around with the clamp meters at the end of the job doing pretty much what you are doing.
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