Hi @Yauci86 and welcome!
What you are describing looks like a Pokémon GO rebalance. There have been several reports similar to yours of late, please see an example here:
There are places in the world that do not respect Pokémon GO density rules due to past abuse and if my recollection from the Spain challenge is correct, there were multiple such locations in the Canaries. The wayspots are progressively desyncing from Pokémon GO and then coming back with normal density rules. Unfortunately that results in less Pokéstops/Gyms than the unusual situation you previously had.
I understand that your community and you got used to the cluster, but unfortunately it is unlikely to come back as what you currently see corresponds more to what other people in the world are experiencing in terms of density. The fact that as you say they are still present in Ingress or Lightship further suggests this is not a removal but a Pokémon GO-specific desync. I would strongly suggest not nominating them again as they will always be marked duplicates, they are in the database, just not eligible for Pokémon GO. Sorry for the bad news.