Just asked at the Migros customer service desk today and found out about it. Seems to be a bit of a hassle as officially it is not a deposit but a "rental".

In short: If you still have the certificate (prerequisite), then you will apparently receive a partial rent of CHF 10.00 back at Migros from next week.
Normally, you would have to contact Sodastream directly (but they will deduct CHF5/year used from the rent paid). However, you will get at least CHF10. - will be refunded.