Thanks, with Commands > Clear Caches it works.

Just for your understanding: I use a software, which opens tunnels over one or several jump server and it opens WinSCP automatically with the IP 127.0.0.1 and the port from the tunnel. Because of that WinSCP sees same adresses for different servers.

There's a symlink cache per server. Though I do not understand why it would be problem in your setup. Anyway, you can clear the cache using Commands > Clear Caches, or you can turn the cache off altogether.
See https://winscp.net/eng/docs/directory_cache

I have several projects with user directorys. For example:
Project A with server 1, server 2, ... have the common directory /home/user/tom, which links to /server1/home/user/tom. I save the shared bookmark /home/user/tom.
Project B with server 10, server 11, ... have also a common directory /home/user/tom which links to /server10/home/user/tom. When I open the shared bookmark for project B /home/user/tom, I get an error message that directory /server1/home/user/tom doesn't exists. Somewhere WinSCP memoriezes the "real" directory behind the saved bookmark.

Could you fix the bug?