Take a look at this link for more information on upgrading from 3.3 to 4.0. The link provides some caveats to consider before pursuing the upgrade (i.e component matrix, hardware support)

http://www.cisco.com/en/US/products/sw/voicesw/ps556/products_field_notice09186a0080229a8b.shtml

I would also recommend that you backup the Publisher's database before going with the upgrade.