Stu
The series adopter may accept the 41mm filters as drop in series VI 'clones', e.g. a series VII filter adopter can also accept (some) 49mm filters as drop ins. You could then mount the 41mm filters on the 39mm lenses + adopter, though it might 'screw' your hood arrangements for the 39mms.
The problem in your case is tolerances - the 41mm screw in may be too large in diameter the series VI nominal filter outer ring (40.3mm or so) drops in to a series VI adopter with a 2mm or more diameter clearance (42.5mm or so) your filters might not even drop in, but leitz filters (that I use) are normally small so you might get away with it, depending on filter and individual series ring tolerances.
There is a 2nd problem some 49mm filters are too large front to back and need grinding to reduce their depth, to allow the securing ring or hood to thread in to the adopter.
But you are desperate that you might grind leitz origionals?
You need to buy a holder or at least try to borrow a series VI holder or lens, borrowing a holder only needs to demonstrate it might fit a 2nd ring. It the filters are tight you might be selecting for an adopter larger then normal. You might accept a ring that needed filters to be pushed in?
I know my Leitz series VII kit will take some of my Oly 49mm filters, this only saves me money... it involves turning a gadget bag upside down before I set out. I have even thought about a 49mm pola filter in a 35mm rotatable lux clip in hood, this involves scrapping the 49mm pola, as I have spare linear 49mm pola filters... No sun here today so I'm not going to try this.
Joe tells me this series thing is easy...
A 39mm filter would fit into a series VI ring apart from front to back depth...
Noel