Thank you for your post.
I am unable to replicate the issue. Here are the steps I took:
1. On my Mac with Mac OS X 10.9.2, I launched FileMaker Pro 13.0v2 and opened up a few test files.
2. From the File menu, I selected Sharing -> Upload to FileMaker Server...
3. I selected a Mac OS X 10.9.2 machine running FileMaker Server 13.0v1.
4. The current file was selected, I clicked Browse, added two other files, and then clicked Upload.
5. I then launched Safari, and launched Admin Console of the FileMaker Server machine. I see all files listed and opened.
6. I selected one file and closed it.
7. With that closed file still selected, I clicked the trash can and confirmed deletion of the file. All other files are still listed and opened.
8. To verify the other files were open, with FileMaker Pro 13.0v2 still open on my machine, I remotely opened each of those files.
Let me know what I'm doing differently than you so I can try to replicate the issue.
that server was also running since the update to 10.9.x until I had to replace one file
Since FileMaker Server writes information to the OS, when you updated to Mac OS X 10.9, not everything may have been accessed correctly.
Since this issue has occurred, have you tried uninstalling and reinstalling FileMaker Server after updating to Mac OS X 10.9.x? If not, copy your database folders to the Desktop, uninstall and reinstall FileMaker Server, and then set up the Database folders and copy the files from your desktop to their respective folders.
Launch Admin Console and see if you are now able to remove one file.
as mentioned in the original posting, restarting the server machine helped.
Sorry, I did not mention in the original post that I can remove a file, that's not the problem. After removing the file, the admin-thing (how does one name this?) didn't work anymore. After the restart, everything was ok.
Since we encountered the non-working 'admin-thing' a few times, I believe that there might be a problem with that - when running for a long time without restarts