The cleanest way to approach this fact pattern is to separate it into a validity question and a rights question, and to pay close attention to the retrospective effect of the new requirements, since that is where the real constitutional problem lies.
On validity: a waqf created decades ago through open, continuous religious use is already a completed legal fact under the doctrine of waqf by user. The new Amendment does not merely regulate how future waqfs are to be created, since if it did, it would raise no serious constitutional problem. The concern is that, applied to existing properties, it would reach backward and unsettle dedications that were valid when made and have remained valid ever since. Courts are generally reluctant to read a statute as retrospectively destroying vested rights unless the legislature says so in the clearest terms, and even where it does, such retrospective application to religious dedications invites the strongest constitutional scrutiny.
On rights: once the property's status is threatened, four distinct constitutional protections come into play, each addressing a different aspect of the harm. The community's ability to continue worshipping at or maintaining the site touches Article 25. The community's authority to decide, on its own, how its religious institutions and endowments are run, without a new precondition imposed after the fact, touches Article 26(b) and 26(d). The unevenness of applying a deed and duration requirement to Muslim waqfs while comparable Hindu and Sikh religious trusts face no equivalent condition touches Article 14, since a classification that singles out one religious community's endowments for a stricter procedural burden needs a rational and non-discriminatory justification, which is difficult to locate here. And if the end result of enforcing the requirement is that the property changes hands or loses its dedicated status, that final deprivation touches Article 300A.
Taken together, the property is genuinely at risk if the Amendment is applied literally and retrospectively, and Articles 14, 25, 26, and 300A are all engaged, with the retrospective character of the deed and five-year conditions being the central constitutional flaw.