Regarding 12.04 vs. 10.04, except if you have strong reason to either benefit from 12.04 updates (and even in such case, I would look at back-ported solution) or if you do need GPO or Kerberos, I would, at least for the time being, not move to Zentyal 3.0 but wait for 3.2
I may happen that 3.2 is somewhat different, from an architecture standpoint, from 3.0 (which is very different from 2.2, reason why migration is not easy)
As Zentyal home user, I'm pretty happy with 2.2. I made some tests with 3.0 but have not been convinced that is was worth the migration coat.
Debate could be somewhat different for medium organization for which better Windows domain emulation (including GPO support, even if with some limitation) does help but I still can see the point for small business and home users.
back to your question: in order to backup samba content, you may just copy folders elsewhere, either on external system or even on your server. Do not forget mail (/var/vmail if I'm not wrong).
Once done, you can remove and purge existing Zentyal packages and reinstall 3.0 from scratch, recreate accounts, copy back your data. In the worst case, you may have to change ownership or apply access rights.