Contacted AMEX today to request a chargeback of the representment. Spoke to a really nice agent who actually took her time and looked into it properly.
The reason AMEX reapplied charge was due to the fact that ""The ticket is non refundable. Merchant has offered alternatives as rebooking of the ticket or the travel voucher."
I am disgusted by Swiss, not only did they say to me on the phone "Yes, no problem, you are in the queue but we are not processing refunds at the moment" but they also lied to AMEX as the flight was actually cancelled, there have been no flight to my destination (LJU) since March and there are still no flights there until the end of June.
AMEX has now reopened the dispute for me to submit the documentation, Lets see what happens now.