Sadly, stories like yours are becoming all-too-common.
As certified XLR techs become scarce and techs in general have minimal experience working on the XLR's folding top, they completely lose it when a Tech 2 doesn't give them a fault code and begin to plug and chug parts (and try to train themselves) on the owner's dime. As you already know, the hydraulic pump is anything but cheap. The tech 2 can measure a lot of pump-related parameters to gauge its performance without it throwing a fault code.
If your symptom elaboration is thorough, the pump has nothing to do with the auto cinch latch that pulls the rear deck lid into place when its switch is tripped. There may be other issues at play, but the pump wouldn't be a suspect for that kind of problem, since it's electro-mechanical and isolated to a specific function. (Drawing the deck lid down at the end of the movement cycle.)
The front tonneau cover (what you call the "black flaps") intermittent operation is probably related to a position sensor, but without seeing the position count values stored in the folding top control module, that's just me trying to make an educated guess based on the how the folding top operates.
It makes no sense to have a car sitting at a dealership while they scratch their collective heads for this problem, unless they are clueless. Troubleshooting the folding top isn't black magic or rocket science.
But being able to drink beer while working in the garage definitely makes the process smoother -to a point for me.
CC
