Very simple.
The Republic of Cyprus, that is officially most of the island except the British territories, joined the EU as a whole.
A part of the Republic is under Turkish occupation, though, and the Republic has no actual control over it. So when the Republic joined the EU it was specified that the EU laws are suspended on the uncontrolled territories until the conflict is resolved. So while the whole country joined the EU, it only actually “works” in the territory that is actually controlled by the country.
And while joining the EU is indeed a complex process, it doesn’t actually *require* for the country to control the whole territory, nor it creates any difficulties that are impossible to overcome. Unlike, say, joining the Schengen area. Since it doesn’t have any border control within the area, you can’t really join Schengen if you don’t control your own borders. Otherwise anyone could enter the area freely through the uncontrolled territory, which is something that’s not allowed, obviously.
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