Flashing new rom, are old files deleted or hidden? I'm not sure whether I'm doing something wrong or it's something normal.

I had CM9 on my Galaxy s3 and decided to try another rom (Paranoid). I didn't like the new one I installed and downloaded another (Carbon). But I am noticing that my internal storage is close to being full now. But when I browse the phone from my PC, I'm not seeing anything out of the ordinary.

I copied Carbon zip onto the phone, but clockwork mod is not even seeing it, I am noticing a lot of files from the sd and I'm still seeing the Paranoid zip from clockwork mod, but I cannot see it from my PC.

Did I skip a step somewhere? What should I do?
What happens to existing files when flashing a new ROM very much depends of the location in question:


your SDCard (internal or external) is not touched at all, apart from the fact you're placing the update.zip for flashing there.
your internal storage (/data and /cache) is neither touched by the flashing process itself. But when switching between different ROMs, it's recommended to wipe these two to avoid complications
some other locations are usually wiped and rewritten. This includes for sure /system, and in most cases also /boot


I know of no case where files are "hidden". Either the entire partition is not touched at all, or it is wiped. It might be that on some partitions files are simply overwritten, though I've never heard of such a case either.