If the Loft Conversion was completed in 1999 then it would be the rules that applied at that time that would have been followed by the Builder in charge of the build.
You will not be made to comply with the new rules.
Check with the council if they have a copy of the building officers notes, if so then you will know what happened during the construction of the Loft.
Our advice would be to pay the outstanding fee and make good anything that failed the Building Regulations requirements and get the Completion Certificate.
