It would appear that you have done everything by the book, although it is the Promotors responsibility to notify the Council that you intend to start work, not viceversa. I understand that you delegated this task, and I get the impression that it was delegated to somebody recommended by the developer, who obviously failed to do their job.
1) Keep your fingers crossed, and play along with the Council.
2) If you do not get your property legalised by the modification of the Council Planning Regulations, report the Architect to both the local Architects Institute, and to the “Consejo Superior” in Madrid.
The Architect should have advised you that your land was not “Urbanizable”, should not have commenced works without a Building Licence, and should have completed the “Asume de Dirección”, which notifies the Council that works are to commence under his or her supervision.
Although it is probably a bit late for you, I would advise the following for the benefit of others on this Forum:
A) Don’t believe anything that a Developer, Builder or Estate Agent tells you. Get it in writing, and checked by a Lawyer.
B) If you need an Architect, go to the Local Architects Institute and ask them to recommend one. Do not hire professionals (Architects, Surveyors or Lawyers) recommended by Developers or Estate Agents. Their interests do not coincide with the buyers interests.
C) It is the Promoters (ie Owners) responsibility to make sure that what they are building is legal. If Power of Attorney is delegated to somebody, make sure that they are not related to the seller or Estate Agent.
In Catalunya, foreign buyers who intend to build their own houses or renovate existing ones are lucky enough to have a Clients Advisory Service within the Catalan Architects Institute, where they are attended by an English speaking Architect who will advise them on exactly how to proceed. They will also be sent a list of English speaking or even British trained Architects who are registered in Catalunya, if required by the Client. Unfortunately, I don’t think this service exists elsewhere.