As i see it's due a the java.exe process mostly, which is using the folder.
To resolve this prob, first download "unlocker" (Google for it, it is free ).
When u install Unlocker, try to upgrade the SDK again and when the alert message ll be shown just do followings :
1/ nvigate to your Android Sdk Folder
2/ with the right mouse buttom click on Unclocker (it will show u all process using the folder into a form, just select kill all process).
3/ redo the upgrade of the SDK and if the alert box apprear again redo the steps (this prob is common and i used to do like as i told u).