The general position is that in order to lawfully build on land you need both planning permission and the appropriate property rights, and the two issues are normally independent of each other. (The most common exception is if you have a covenant that forbids applying for planning permission, or forbids objecting to the grantor applying for planning permission on their retained land.) So a possible breach of a covenant would not normally be a material consideration in a planning decision. (There are always exceptions such as when the case for granting planning permission relies on delivery of enabling infrastructure and a covenant would prevent that.) But of course in practical terms there isn't much point in spending time and money securing planning permission if there is an obvious likelihood that the actual building project will be blocked later by a covenant issue. All of that is just background to saying that this is a planning community page, not a property lawyer page, and your probably in the wrong place for advice on covenants sorry!
