The first point for the developer to appreciate is that planning permission does not override the covenant. The planning authority will usually only consider the application in respect of its planning merits and will not consider the private rights as between the respective parties. This can also often be a source of confusion to the person who has the benefit of the covenant and who is intending to object to the planning application.
The developer should then check that the covenant still affects the land. Usually, this can be confirmed at the Land Registry where extant covenants will be recorded in the Office Copy Entry for the property. If the land is unregistered it may be more difficult to establish whether the covenant still has effect especially if it was granted many years in the past.
The developer should then find out who may have the benefit of the covenant: anybody who currently owns any part of the land originally benefitted by the covenant will be able to enforce the covenant provided they can show that the covenant benefits or preserves the value of that land.