I left it uploading and when I went to look at it the screen was blank as if it had turned off. I thought it had shut down to restart itself and realized it was not doing anything. I tried to restart it but now my desktop manager keeps telling me to connect my device and it is connected
If Application loader is not seeing it, you may have to re-install the BlackBerry Desktop Manager package. The reinstall should correct any USB drivers errors.
If that does not work, you may have to force it to rebuild with a manual command.