batch pre processing

Hello every one
I am trying to batch pre process data from several nights. Inbetween nights I dismantle my set up so camera (DSLR) orientation gets changed. I have 2 questions

1- Does batch pre processing script sorts out automatically all the flats which correspond to a given set of lights taken simultaneously if I am processing data taken over several nights but lights and flats taken together (i.e. camera orientation does not change)

2- What happens if camera orientation has changed between my set of lights and flats over several nights, would batch pre processing is the right thing to do.

Thanks

Saqib
 
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