Hi Joerg,
Sorry that you hit this error. There's a bug parsing a particular version of the Skyline file format. We've already fixed it but still need to get it deployed to PanoramaWeb. I can update this thread after the upgrade.
https://www.labkey.org/home/Developer/issues/issues-details.view?issueId=48689
In the meantime, you may be able to get Skyline to regenerate using the latest format as a workaround. You can try going to "Edit > Manage Results > Rescore" and then importing the updated file.
Thanks,
Josh