Sheep and goats should keep their flock and individual numbers from the holding of their birth for life. That means any sheep/lambs you buy in (as in born somewhere else) will come with their own flock/individual number and any that you breed on your farm will get tagged with your personal flock number and individual number. Sheep and goats have the same flock/herd number, pigs have their own again and I guess the poultry one is coming from a different authority again.
It is a good idea to have a note (and it should be in the movement forms anyway) of all your sheep ear tag numbers, when they loose a tag you can order a replacement tag with the same number (and yes that means with someone else's flock number on). Happens all the time with pedigree animals, as the original number is on the certificate. If they loose their tag and you don't know the original number they will get a RED tag, which again has your numbers on it, but RED means that the sheep's origin is not verifiable anymore. If they are homebred (and not pedigree) I think you can just allocate the next number of your tags and cross-reference to the old number in holding register.
Not quite sure where chooks come into this, as I never keep more than 49 on my holding...