Lufthansa, Bank and SEPA mega mess

Oct 9: I booked a flight in lufthansa.com, and paid via SEPA (never used it before), which asked for my IBAN. I received the confirmation email (booking code and e-ticket no.), so far so good!

Oct 12: I received a winbank email alert from the Greek bank, saying that the payment (338.26€) was unsuccessful/rejected. I called the bank, and they told me that indeed, the payment will not proceed (because of something related to the capital controls Greece had). I had checked and Greece is part of SEPA.

I called Lufthansa, right after talking to the bank, inform them, and confirm my booking. The operator said, since you have the booking code and e-ticket no., you have nothing to worry about, everything is OK.

I am now worried of a scenario where I am going to take my xmas flight and they say, oh your booking is invalid (is that possible?).

So, what should I do next?

Posts like this make me more confused: Flight booked but card not charged.

PS: Lufthansa SEPA payment method (SEPA payment if you are resident in Germany.) <-- I am not, I am just in Germany now!