Question:
Someone on our side entered the the wrong readings for a meter, we noticed it and deleted it. We then entered the correct reading, deleted the old bill and then ran it again. The rest of the meters are fine, but the reading on this meter still comes trough wrong.

Answer:
It is probably old interpolated profile that is stuck in the database.
To clear it, select the meter, go Edit->MeterTotals, and click on 'Re-interpolate All'.
That should fix it. After that, you can delete and rerun bill for this meter.