I copy images/videos/music to a usb hdd and when after viewing, I delete them (using my media player).
If and when I connect hdd to computer before starting the computer, I always get that 'checking file system', but on (usually) F\. Its 'cause windoze did not delete anything and is down for the count. (←Press any key in X seconds!)
Occasionally, programs change/modify files/registry settings and windows only recognize these changes at startup.