I don't think it will be a problem. You don't have to 'register' your animals as such ie individually, rather the authorities need to know that you keep sheep so you can be sent all the relevant info, especially if there is a disease outbreak.
You keep a record of your sheep numbers and movements in your flock book, and they keep a tally of animals on and off your holding from the movement docs you send in (which isn't the same as your overall numbers). But I think that when you set up, you have the sheep you have if you have taken them on as sitting tenants and just let them know. If the previous owner hadn't been in the system it isn't your friend's fault and they will just be pleased that he is doing things properly now. That is the case in Scotland anyway.
So you register your land as a holding, and you inform them that you keep sheep, or cattle, or goats or pigs, but registering animals is really more for pedigree stock which are registered with a breed society.