Yes, it matters.
Check there are not two sheep missing their ear tags. The UK number is the flock from which the sheep originated (so all sheep from that flock will carry the same UK number), the individual number obviously is specific to that animal, so the pedigree cert is only for the animal with the eartag which matches exactly what is written on the certificate. From past observation, it is possible (but unlikely) that the breeder made a mistake when putting in the tags, or has given the wrong certificate when selling that animal. Check the movement document which came with the sheep which should (in England, I think) record the individual tag numbers of the sheep which arrived. That way you can check whether you do have an animal with a number which exactly matches the pedigree, unless the numbers were recorded from the certificate, not from the actual ears...in which case it's still a mystery.
All Soay registrations are recorded in The Combined Flock Book of the RBST and if you are member of the Soay Sheep Soc you have access to that and can look up to see if the sheep with the certificate you have (if you don't also have it yourself) is owned by another member. Before you do that perhaps you should check the whole flock for their tag numbers so you know exactly what the situation is. If you can't work it out then in theory that sheep is not registered.
I don't know the rules for re-tagging in England. If you are still stuck then check with Julie Suffolk.
Wretched eartags indeed