Jacob Blevins - without seeing the assembly and or your feature tree, the answers to your question could be wrong or vague at the least.
The most important portion of designing with Solidworks is here.. The Design Intent Thread Depending on the Design Intent and the assembly layout the nest thing that comes to play is Skeleton Sketch Part Method for Large Assemblies
To take a stab at your issues, the first thing I would say... It's possible you have Circular Rebuild Issues or parts designed in context within the assembly and there are related parts missing or changed etc..
I have the same issues, except the appearance disappearing one. I had an assembly that worked has been functional for days. I opened it today and 3 parts were just randomly thrown somewhere in the assembly. I would open the hinge assembly where a part went missing and it looked perfectly fine. When I broke the assembly down to it's individual parts there was a subassembly that the part for no reason at all went missing.
I also have assemblies where parts litrerally disappear! Not hidden, not suppressed they just vanish gone! Put the part will still be listed in the tree. So I try to open it on it's own and it is invisible not there, can't select it, no build tree only the file name. So I end up rebuilding the missing part put the new part in my assembly. Then randomly some other day working on the assembly it will reappear causing mating issues, and problems. Worst part is you can't see it, because now it has a new part directly on top of it.
I have only found it when I try to fix the problem mates and low an behold it just happened to reappear. It is really pissing me off, that everything I make blows up for some stupid random reason. When I was in school, we built complex assemblies and never had a problem ever! This version at my work is a turd! It just randomly does whatever it wants.
I just had a hinge that opened from 0 degrees to 72 degrees. It was working fine no problems. Open it today it wouldn't open. I checked the mates and the angles were still fine. Then I bumped the hinge in the wrong direction and it opened 72 degrees the opposite way, and I can't fix it! I tried reversing the angle. Nothing! What did I do since it worked? I saved it yesterday and opened it today!
I am really tired of these unexplained glitches, and worse I am tired of my boss asking me to open models, and it isn't working, models blown up, pieces everywhere, parts invisible and I have no explanation, so now I look like the moron.
I am wondering if my company got sold some crappy Solidworks software. Like I said when I was in school I never EVER ran across these issues.