The files found in ~/Library/Application Support/OnlineBackup are temporary files. The online backup software packages your data before upload. After the data has been backed up, the temporary files associated with your data are deleted. All temporary files in ~/Library/Application Support/OnlineBackup are automatically deleted once the online backup software is running and all files have been backed up. You can also manually delete the temporary files.
If you are looking to change the location of these temp files, you can create a symbolic link for the online backup folder and point it to another location on your computer.
ln -s path_to_new_temp_folder ~/Library/Application Support/OnlineBackup