As you say the important thing is that roof works now and it did not cost me anything other than my time. I am still a bit worried it might throw a fault at some point as you are pretty sure it was motor but I think it was latch microswitch. Weak battery might have played part as well if the roof was operated with the engine not running and voltage dropped under load and motor draw too many amps.
There are several reason I think motor or in fact the whole pump has been replaced some time in the past. I already mentioned that motor looks very fresh inside but it could be due to roof being used very little not because it was replaced. Other clues are oil under pump and it's old dried up sticky oil not fresh leaks so I think it's the oil that escaped from hoses when replacing pump and not cleaned up. The last one is 'Approved' sticker on the pump which I think might mean approved warranty claim replacement.
The sliding flap does have at least one tab/pin broken, I can get it partially closed but not fully. It's best just to replace it. New one from dealer £86 but I have sent messages for several sellers breaking A4 Cabriolets for parts on e-bay for a price quote.
All the garages are closed on Sunday so I went to Halfords for their free AC check. Does not seem like they now what they are doing. Opened bonnet, they had a look said they cannot do anything and I need to go to garage. I asked why - they could not find ports. I showed them where they are, they connected bottle with the gauge, it showed 0 pressure in system so advised that system is completely empty and while they can charge it for £50 it could all escape very soon and stop working again. I decided to try my luck. So they started filling it but when pausing filling it would still show 0 pressure in system so he advised to stop filling as it looks like there is a big leak and whatever he fills in escapes straight away and did not charge me anything. Went home checked pressure again on VCDS, it now shows 4 bar instead of 1 so it does not escape as soon as fast as being filled in.
If fact now it has enough pressure to start AC but not enough to provide any meaningful cooling. Will check pressure again tomorrow again to se iff it is dropping and how much also it is hard to judge part filled system as the pressure will change considerably depending on ambient temp.