Hi, thank you reporting this problem to us. The current version of WWWBackup was not designed to backup USB drives. However, it should have no problem backing up a USB drive. The only problem is as mentioned in your message: the drive letter could change, esp. if you have multiple portable drives, and if you plug & unplug very often.
Now please note:
(1) DriveHQ can skip file upload / download if the files are the same in the source folder and destination folder. So even if you re-create a backup task, as long as the task name and source / destimation folders remain the same, it won't upload all files again. It does take a while to compare files for any changes.
(2) You can manually re-assign a drive letter to a USB drive. Please make sure no files are open in the USB drive. You can then click right-click on My Computer and select Manage. It should open Computer Management window.
Select "Disk Management" in the left-hand side. Right click on a drive letter and select "Change Drive Letter and Path". You can change the USB source drive to the original drive letter when you created the backup task.
DriveHQ is working on a new version WWWBackup to better support USB drives and network-mounted drives.