As I'm understand is that when a gate is closed and you haven't enough clue token to seal it this turn, you may seal it in another turn.

1) In which fase can you seal it? We do now in the Arkham Encounter fase.

2) What happens if in the meanwhile in the Mythos fase a gate for the just closed location is drawn? We play it now that that is bad luck and a new open gate is put in this location, but is this the way to do it?

thx

You are wrong.

You cant seal a gate in later turns. "Immediately" says so . And nothing even hints at the possibility that you can.

Arkham Rules p.17, "Sealing gates":

If an investigator successfully closes a gate, he may immediately spend five Clue tokens to permanently seal it.

If you close a gate without enough clues to seal it, you can't then seal it later - you have to wait for another to re-open.

Sometimes it's better just to leave the gate open, grab some more clues, and go back through it to try again. Other times, someone else might be able to pass you a clue-generating item (Old Journal, for instance) that you can use while still standing on the explored open gate - and then you'll have enough clues to close and seal.