Loud clank sound when soft top compartment lid closes

It's probably a broken plastic part inside the hinge that is used to secure it in the upright position during servicing. If that's it, you can simply cut it away. Like I said, it's only purpose is as safety catch when holding the cover upright while servicing the hydraulics.

I used to have a photo, but can't find it. I did find a photo in this post:

Yes it's a plastic arm in the middle of the cover hinge (one on each side). See that post I linked. There is a photo there showing the broken plastic with the arrows. Not that On either side of the hinge, there are plastic "ears" that can be rotated toward the front or back of the car. For normal use, they should be rotate to the rear. When you are servicing the system, they are rotated toward the front, which puts tension on the plastic arm inside the hinge so that it will keep the top cover open.

The arm should not be able to be rotated. It's supposed to be a solid piece, but when it breaks, its halves just flop around and can then get caught in the hinge as it articulates and that's the popping noise. In that case, just cut it out of the hinge. I used wire cutters to snip off the flopping arm pieces on mine.

Another possibility is an alignment issue with a small "hook" on the cover flaps.