I don't think the problem is with how much you uploaded to the Cowon. I uploaded 130GB in one go without problems.
I suggest you try two things. Go to Settings and then on page 3, try "Database update". If that doesn't work, go to page 4 of Settings and click on "Information". From there, format the HDD and then re-enter your music. Don't format the Flash. If both fail after doing the two things above, update your firmware from the Cowon site. It gives you precise instructions on how to do it.
It will all be fine...I am sure. Good luck.