You can try to recover your seed from the serverlog files. They should be located in the same folder as the server.ini file. On Windows it should be here:
%AppData%\Roaming\Avorion\galaxies\<your-galaxy-name>\
There should be several serverlog files. Pick one with a date prior to when the seed went wayward(should be included in the filename). Open the log in a text editor, such as notepad, and search for "seed". Copy that seed into your server.ini, then restart your server. You should be good to go.