It depends on the type of aircraft being refueled.
If you are asking merely for curiosity then the simple answer is it is calculated before refueling begins, and usually fuel is only put in inboard tanks or locations that don't affect CG (center of gravity) much.
If you are in the industry of air refueling then this question should be asked of your instructors.
Usually the PIlot's Operating Handbook (POH) for the specific aircraft will have an entire chapter dedicated to weight and balance issues, which will also include the effects of various fuel configurations. Any major change in the aircraft affecting operations will result in an amendment to that aircraft's POH. Quite often two aircraft will appear to be identical at first glance will have different POH data based on installed sysems.
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