My Copen opened the windows the last time I put the roof down. When the roof was put up, the windows would no longer close. I have tried roof up and down several times, but nothing changes. Could it be a fuse? Are the windows fused separately? Is there an interlocking switch somewhere?
Is the roof warning light to the left of the Air Con slider lit? If it is, the roof is still registering open, check it's fully up and the catches locked in place. It could be the switches in the roof catches.
Y I assume you have you tried operating the windows manually when the roof is up? Because that’s how you get them back up after having the roof down. Do the windows work when the roof is down??