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When I restart the server with the start .bat, nuxeo.xml is updated with new features that I wrote in admin center, but if I restart the server from browser (admin center) OR from window services (I have installed nuxeo as windows service with your guide: http://doc.nuxeo.com/display/ADMINDOC/Installing+the+Nuxeo+Platform+as+a+Windows+service ) ... why?
There's no start.bat script. Did you mean Start Nuxeo.bat? It cannot be used for a restart. It's only a convenient shortcut to nuxeoctl.bat start.
start.bat
Start Nuxeo.bat
nuxeoctl.bat start
nuxeo.xml comes from the templates. If it's not updated in some cases, that could mean:
nuxeo.xml
nuxeoctl configure
Try to investigate a little more and provide some debug information. Cheers.