If you keep data about a person in the EU that data is protected by GDPR regardless where or how you got it, having an intermediary doesn't matter.
> how will the Council know if the end-tracking companies deleted their data?
That doesn't matter, all they need is to ask the companies and the companies to say that they deleted the data. That is how everything else works with GDPR. When you ask a company to delete your data you don't know the company deleted it, they could still store it but keep it hidden etc. The government asking this is exactly the same.
If it later comes up that companies has a lot of data about users that they can't explain how they got, or that traces back to this case where they said they deleted it, then those companies will get huge fines. Open violations of laws where there is no question that the company knew they were breaking it are a very different case from companies toeing the line, the fines would get much higher.