Hi Lambo1, whereabouts are you based?
Loom problems are very common, especially in the section that flexes every time the door is opened, I guess that's where the repair was done? A new door loom bought and fitted shouldn't cost £400 though, that sounds very pricey indeed.
It could be moisture related, and corroded connections between loom and motor module, but inspection and cleaning are the only way to test that really. Could also be water ingress into the connector(s) at the a-pillar, as it's only the rubber bellows/boot that waterproofs that area, and they can be misfitted easily if removed for inspection/rework.
Check fuse number 11, if you haven't already.
However: the window motor modules in your car are from an era where they have a poor reliability record, in my experience.
The same types are used in very early mk2 Fabia, late mk1 Fabia and VW Transporter and Polo 9n3 models, all of which suffer similar problems. The units in drivers and passenger front doors communicate with one another down a single-wire 'LIN bus' data connection, which doesn't connect in to the car's overall diagnostic system, so errors/faults in either module are 'invisible' to the car at large. I'd be very surprised indeed if the fault is with the body control module, as it has very little to do with the window motor operations.
The driver's side module is the master and the passenger side is a slave unit, problems most often seem to be fixed by replacing the master unit (unless loom/fuse causes are to blame, obviously). They tend to be correspondingly more expensive secondhand, and with fewer available.
I expect yours to have part number 6Y1959801. There's a suffix 'SK2' in the parts catalogue, but its not clear what this means, and they don't print it on the part number label on the product, only on the box it comes out of; so secondhand purchases can be a bit 'hope for the best' unless the seller is crystal clear about which vehicle the part was removed from.
@Bertie90 has recent experience of this stuff, in a similar age Roomster, so he may be able to offer some tips that haven't occurred to me.