I've heard it said that the pressure-limiting valves in the pipe run to the rear brakes can cause problems if the system has been completely emptied. They are at the highest point of the run so air bubbles can stick there.
The advice is to jack the car up as high as possible at the back, or park facing downhill.
My standard advice at this point is never to drain the entire system at once. Seal off each section, bench bleed the components, and bleed air out of the joints as you re-connect them.
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