I've done this! 3 times on 2 cars, and I agree, it's a pain.
As chb says, it's very difficult to remove the upper piece of trim under the doors without breaking the clips. Basically to do it, I start at the rear by pushing a thin screwdriver between the sill and the upper cover and you should hear a click when you find the right point. There are a series of clips all the way along, every 3-4 inches or so. I unclip the lower clips of the upper cover all the way along, such that the upper cover can pivot on its top clips, if you see what I mean? I then use a T25 Torx bit on an extension bar to thread between the sill and upper cover and undo all of the Torx screws. The rear end cap is then removed by undoing a Torx screw under the upper cover, 3 inside the wheel arch, and one underneath the car. The rear wheel needs to be off for this. The end cap pulls out towards the rear of the car. Next, you need to remove the front wheel and undo the 3 Torx screws that attach inside the wheel arch. There is Torx screw on the front door jamb which also must be removed, it's near to the upper cover. Then, all of the Torx screws underneath can be undone, they screw into the floor via plastic retaining nuts. The sill should then be able to be lifted away from the car. Now, the upper cover can be separated easily without damage, and the screws retrieved.
Refitting is the same process, reversed. Just only press the upper cover into place on your are happy all of the screws are in place. Make sure not to tighten them too much, as many thread into plastic and the thread could be destroyed easily. It's the type of job where if you estimate 2 hours to do it, double it, at least.
I've removed the 6 sections of upper cover over the 2 cars, and only ever had to replace one. I have broken clips of course, but the ones that have broken have not been at the ends, and so do not affect the security of the cover as such. It's certainly possible to do it without breaking clips.
Hope this helps.
Regards,
Matt.