I think the fuel scoop bleeds the energy from your shield as you close on the star and converts it to fuel.
Honestly if you think too hard then the weapons wouldn't work because they would be inside the shield.
Just think of it as being to advanced, in the physics realm , for our brains to comprehend.
As the whole mankind knows since the elementary school, shields have a frequency, which can be modulated. So, it's no problem to synchronize them with the weapons and shoot through them. Like in the 1.WW with the machine guns shooting "through" the propeller of the aircraft. When you know the shield modulation/frequency you are able to circumvent them, like the Borg did. Sometimes, rotating shield modulation can prevent this.
QED.
P.S. : the fuel scooped from stars is just simple plasma, not a mysterious type of energy conversion from the shield. Strange idea, btw. You would have known this, when you not have slept in the 2. Class of the elementary school. Sit down, F!
P.PS: my brain can compete with every physical problem you may think for!
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