At print time in e-z Cert, for express applications that you print after your chamber has stamped the document electronically, you will be shown the time period for storing certified documents. The current rules are:
EC Certificate of Origin - Keep the pink copy for 2 years
Arab Certificate of Origin - Keep the blue copy for 2 years
EUR1 - Keep the white copy for 3 years
A.TR - Keep the white copy for 3 years
For those documents it is the hard-copy that you need to keep or you can return them to your chamber if you would prefer them to hold it.
Regarding invoices, I believe the recommendation from HMRC is to keep them for 6 years but this can be in an electronic format.
Hope this clarifies but please come back to us if not.
Ian James (e-z Cert support team)