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The flight logs should not affect anything. There is nothing limiting the amount of area you can collect.
Do you have a screenshot of your setup?
Are any of the points in your survey area more that 2km from another point? That is what triggers this.
The other part of this error message is a recommendation to reset your home point. You might just have to give the aircraft a bit longer after a battery swap so it will set its home point again. When you hit the "upload" button Map Pilot attempts to set the home point.


