When filing this return on CORE you will follow the same procedure as you would follow when filing a normal B1-annual return. When filing in the B1 the annual return date to use is the actual annual return date for the company (you do not input the date of the extension). Therefore the shareholding etc. on the B1 should reflect the shareholding at the annual return date. (e.g. if an annual return date was 30 September 2016 and the Court Order extended this to 31 July 2017 then the ARD on the return will be 30 September 2016 and the shareholdings, shareholders at that date must be detailed even if there was a change after this date)
Note if CORE requests audited accounts to be submitted and does not let the B1 be submitted, then you should contact the CRO to remind them to update their system for the extended date as per the Court Order.