If you want to keep copies of your Kobo purchases, download the ePub versions of your Kobo purchases. You can always use the KoboTouchExtendedDriver to convert the ePub to KePub if that's what you prefer to read. ePub is a better format for long term archiving.
The DeDRM plugin for Calibre found at
https://apprenticealf.wordpress.com will allow you to remove the DRM from ePub eBooks.