You may still be a shareholder while not listed in on the B1 Annual filed with the CRO. The B1 lists shares in the name of the registered, or legal, owners and not necessarily the beneficial owners. It is not unusual to have shares held in someone else's name, as nominee, on behalf of someone else. A declaration of trust, a simple one page document, should be drawn up listing the beneficial owner. However this may not happen in all cases.
It may also be the case that the CRO B1 has not been updated to take account of new shareholders.
If you want you can request a copy of the beneficial ownership register which every company is meant to have. However I'd take a guess that it will cause more confusion that anything as this is a new (and pointless requirement for a small private company in my view).