Lowering roof when rear qtr window mechanism broken

[Jez39]

I have tried searching the problems>roof forum without much success so have reverted to raising this as a new problem.
In another thread I have detailed my problem of a broken window mechanism and the trials & tribulations of replacement/repair. I managed to remove the interior trim (to gain access to the window mechanism) without having to lower the roof (and without fully removing the rear quarter panel top trim) but now need to remove the rear quarter panel exterior and interior weather strips. This does necessitate lowering the roof.
Is it possible to lower the roof while the rear quarter window is raised? Or do I have to manually push the window down, and will the roof ECU a) recognise this , b) not get confused and require resetting by Peugeot?
Do you have to immobilise the boot cover as the repair guide says before removing the seals?

[IanL]

I don't know how the roof would behave if you forced the window down, and I think the best thing would be to lower the roof manually. The procedure for manual raising is in the Owners Manual, and I believe it is possible to work out how to lower it manually from that. Once the work is complete, I would raise the roof manually, to avoid possibly confusing the Roof ECU, which has been programmed without taking into account all "non-standard" conditions.

The manual also gives a procedure for raising the roof under power if the windows are stuck in the raised position, but I don't think it works for lowering. It does state that it is possible to move the roof with windows raised, albeit with care.

Lowering the roof manually will involve immobilising the boot cover, so that answers your last question.