I guess I wasn't clear enough. What I meant, about using a temporary directory is to tell the youtube downloader to use a directory NOT MONITORED by MC. Then, once the files are downloaded and combined, you'll have just the good, combined audio+video files in this temporary directory. At that point, you use Windows Explorer, or the tool of your choice to move them from the temporary area to a directory that MC monitors. That way, MC never has the chance to see your "bad" files that are going to be deleted.
Yes, this requires manual intervention. I'm not claiming to be able to automate it for you. I'm pointing out that your method is flawed by allowing non-permanent files to be stored in an MC monitored directory. I mean no offense! But to me that's a flawed methodology. MC is DESIGNED to import all files in it's monitored directories. Allowing files to live there that are temporary is contrary to it's designed behavior. So it's not surprising that this causes a few problems. Right?
My suggestion to turn off auto import was similar. It's to try to prevent MC from importing files that it has no reason to see in the first place.
It's quite easy to disable auto import for a few minutes while your downloads run and then turn it back on afterwards.
Brian.