We started in Admin Console for FileMaker and disabled MBS Plugin. Enabled it again and well, the old plugin is back, even if newer file is in Extensions folder!
Same when we disable plugins for script engine. When we enable again, the same plugin becomes active. Seems like FileMaker Script Engine doesn't really try to unload and load again the plugin.
What works is to use Terminal and the command "fmsadmin restart fmse". This will restart the scripting engine and consequently end all running scripts. But it will reload the plugin from disk and you get the new version.
Alternatively you can of course just restart your server machine or restart the whole FileMaker Server, but that would kill all connections.
By the way, the console app is used to show /Library/FileMaker Server/Logs/stderr as this is a place where the log messages from MBS Plugin show up. Our plugin writes a message on startup as well as any requested trace messages.