Thank you. If the charity has not in practice exercised rights over the roof for the last 20 years and it does not have any expressed rights in its title over the roof, despite the doors, you will not have a right to enter onto the roof which I note you accept. However, if you could show that the charity (its agents and employees) had enjoyed a right of access onto the roof in practice without the landlord's consent, then the charity may be able to claim a right to long use.
Notwithstanding the above, from what you say, the doors have been fitted for some 20 years and as such providing the period is more than 20 years, the charity will have acquired a right to light through those windows over the roof under the prescription act through long use. You may need to check back in your records to ascertain the precise date the doors were fitted as it is necessary for the charity to show 20 consecutive years of use or more in order to claim a prescriptive right through long use to light. Providing the charity can show as much, then any actions the owner takes to limit the light or adversely affect the light coming through the glass will be a breach of the Charity's prescriptive rights and would be grounds for obtaining injunctive relief to require that the owner removes any such obstacles.
If the charity can show more than 20 years of use, it may wish to consider registering its prescriptive right at the land Registry. It can do so by preparing a statutory declaration and swearing this and then making an application for registration. There is no need to register prescriptive writing order for it to be enforceable. The charity can if necessary apply for an injunction using the following form:
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