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I think the dust specks are on your sensor - that's why they are in focus. Maybe you could blow the dust off with a lens blower? You can process the dust specks out - but it would be better to get rid of them, if you can do this without damaging the sensor. The dust is not on your filters, lenses etc - otherwise it would not be in focus. If they are on the sensor it will prevent most of the light from hitting that part of the sensor.
As far as stacking multiple exposures. (I think): Every exposure is slightly different. ie. photons are collected differently and noise (some) is different. By stacking these images you are combining the collected data (photons). If you just stack the same image multiple times you are not adding anything different. Increasing the exposure of subs and the number of subs increases the signal to noise ratio improving the overall image and ability to process it. There are others who could give a much more technical answer than me.
Regards,
Tony.
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