I'm in unknown territory here, but I would be very surprised if there's a protocol for the visit to be "sanctioned" by the DGCA. I'm thinking of MRO's in the UK with multiple approvals from non-EASA administrations and I don't recall the UK CAA, or indeed EASA, being asked or even told about inspection/audit visits from the other administrations, which they would regard, I would have thought, as nothing to do with them.
It is possible, I suppose, that most would let the CAA know as a matter of courtesy only, but not doing so would not affect the visit.
I also suppose I am probably wrong, but I'm sure someone who actually knows about it will respond.
As an aside, if I were you I would suggest to the MRO concerned that they do all possible to help you, their customer, rather than be obstructive. But then I never learned how to be emollient.
Edit: Afterthought; I'm barking up the wrong tree, talking about "Approvals" from other administrations. Sorry! Visiting to inspect the MRO, essentially for its compliance with Part 145, is a different can of worms, and all bets are off. But there's nothing to stop the MRO inviting the Nigerians to look around any time they want to, it's their train-set. Maybe they should just do that and help with the visa invitation, in your interests as a customer.