No worries, let me try and explain.
So you give two book numbers that you thought belonged to Andrew Lindsay from Donaghadee.
You gave R 561990 and R 562162. Those 'R' numbers by way of explanation are seamen's discharge book numbers, akin to a service number, and usually the number would stay with the seaman for his full career at sea. There were certainly instances of lost numbers and new numbers being issued for the same seaman but in general it was one and the same number for every book that he had. So if he left and later went back, in most cases, he retained his original number.
R 561990 belongs to this seaman named Ellison: BT 372/1499/1 -
https://discovery.nationalarchives.gov.uk/details/r/C8368893R 562162 belongs to this seaman named Oates: BT 372/1499/142 -
https://discovery.nationalarchives.gov.uk/details/r/C8369034I do not know what you mean when you say "why are they listed with his book if nothing to do with him"? Could you tell me please why you think they are linked? That is the source of the confusion.
Mr Lindsay's Discharge Book Number would appear to be R 562064, BT 372/1499/65 -
https://discovery.nationalarchives.gov.uk/details/r/C8368957I hope that is clearer, if not, please get back, happy to help.
Regards
Hugh