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Hi Lewis,
A single auto-subtracted dark won't work as well as a master integrated from multiple darks. It will add a lot more noise.
If you dark calibrate twice then you will damage the data. That's the short of shenanigan that could cause the error you mentioned the other day (BPP complaining about no data in some of the subs.)
For flat frames I think you are generally better off just bias calibrating them unless you have a camera with a very high dark current or are doing very long darks. If you do want to dark calibrate them then, again, it is better to use a master integrated from multiple dark frames than a single auto dark though the noise won't have as big an impact because flats have lots of signal.
Cheers,
Rick.
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