Makes no difference whether the choke is between the positives sides of the capacitors or the negatives. The rectifier mostly sees just the first capacitor, since the second has the choke in series with it (whichever way round they are). This should become obvious if you consider basic circuit theory regarding series components.Does this method affect the amount of capacitance "seen" by the rectifier? Ie: does the first choke in the ground run isolate the caps after it from the rectifier as it would if the choke were in the HT line? If not, I could see this as a major gotcha what with exceeding maximum capacitance for a valve rectifier.
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