Resolved!
Thanks for your replies everyone.
The strange thing was that even though the www version of pages did seem to 301 to non-www version (I checked headers were indeed 301), all our pages had disappeared from Google index and rankings too (exept homepage).
The resolution came after we had our host reset the domain to www version on the server to the original state. Within days of changing that, all our deindexed pages (the whole site) jumped back into the original ranking positions in Google with www version and are re-indexed like nothing had happened.
Hope this helps someone else.