Clear the EmonPi backup files and disable it first. You have to removes the traces and the auto built packages to completely make use of the SD card as a new one. Memory card data recovery can guide more on this matter and whether you need to secure certain files from getting deleted accidentally.
A function has recently been written by @emrys which allows users to set a criteria, and delete feed data older than that criteria which should help you. However I’m not sure if it’s been rolled out yet, but if not, I suspect that it will be very shortly…