It is always best to capture your data as close to the same time as possible. If the lighting conditions change (sun to clouds) it may harm your data's ability to be processed well since the features will appear differently.
We would recommend doing the batteries all in a row and charging the first one as soon as it lands so it can be charging while the second one is in the air.
Another possibility is flying a bit higher so you can cover more ground on the batteries you have.
You can restart the mission the next day if you have to though. Just try to do it at the same time of day so the shadows are the same.