Trying to access a server with DNS resolution of AAAA records with IPv6 address results in a connection timeout. Same if we specify the IPv6 address directly. Accessing the same server via its IPv4 address works fine. Nothing is recorded in the log drawer...
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I was unable to replicate the issue with Google Drive on Mojave when specifying 2607:f8b0:4007:804::200a for www.googleapis.com as hostname in the bookmark. Can you provide the IPv6 address if your server publicly reachable?
We have done a bit more research. In general other sftp clients like "Transmit" work without any problems on the same mac os x machine and the same user account. IPv6 connections are only a problem in cyberduck!
During our research we found ticket #8848... It was resolved by putting utun0 on a blacklist of interfaces.
Our machine also implements utun1-utun4 interfaces. So after removing these interfaces the behaviour changes. We do not get timeouts anymore but "no route to host errors" immediately. It looks like cyberduck is still trying to use an interface with no internet connectivity.
Is there a way to specify the interface cyberduck should use for connections?