I stand to be corrected here but, to the best of my knowledge, you can only amend the register of shareholders when you submit your annual confirmation statement.
All of the info on the Gov.uk points to this login page as the right place to be in order to change information about your company:
https://ewf.companieshouse.gov.uk//seclogin?tc=1
So if that's the route you've already taken, I'd expect there to be an option to do so at some stage.
(I've not run a limited company myself since the days when quill pens were regarded as modern technology so, regrettably, I can't advise you directly from personal experience of using the online service. Sorry)
Yes, you can set their shareholding to nil - that's what I did when I tried to edit the shareholder's information, as some of them (30 in a residents' association) had an 'edit' button, but others did not. Just set it to zero and the confirmation statement I was doing went through.