Does it matter if I let my brakes drain when when taking system apart? I'm going to be taking apart a Clarks Skeletal Hydraulic Brake system to try and identify what's wrong with it (trying to remove/unstick a piston), so I was wondering does it matter whether I just disconnect all the fluid cables to the caliper and let them drain, and then do a bleed/refill later?

Most videos I've seen of doing a brake fluid bleed, the system is usually still quite full of fluid, and I can't think of any reason why not but I thought I'd ask whether there's any problems with just emptying the system out.
I think this is mostly a problem in the bottom of the calipers where a hose becomes a reservoir filled with fluid, and perhaps that can get air in there. What I have done in situations like this is to make sure a block is in the caliper and squeeze the brakes a few times before opening the ports to bleed. My theory is that will do it's best to fill the fluid into the air pockets and get the air to come to the top. Of course, it's hard to see inside the actual line so hard to know. Bleeding from the caliper then gets the air out of the line. It's worked for me and given non-squishy levers in the past.