I do believe the two movements are meant to dovetail. The solution is to hold the c after you release the other notes on the loud manual, then pass to the same c on the other, quieter manual, in such a way that they overlap. It's best to do it in a precise rhythmic fashion, moving as quickly as possible to the second manual to make a c quarter note as the first note of the fugue. If the manuals are coupled the transition is made smooth by the same note included in the old and new registration. On Zwolle you can play the Passacaglia on the Hauptwerk and start the fugue on the Rückpositiv, leaving the detail stops set on the other two manuals. I transition from thumb to second finger as I release the other chord notes before I change manuals, then pass to the thumb on the other manual followed by the g in the right hand. Works just fine!
What a great piece and a total thrill to play it on Zwolle with its luminous principals and shimmering 8 and 2 combinations!