I can confirm!
I have just written an update script that compiles the server product then pushes it to the remote server and replaces the existing idempiere server with the new one.
I am using silent-setup here and it works just as expected (Migration from insecure to secured installation).
I'll have to check the migration from secured to secured and hope it will be just fine to copy the .idpass over together with the properties files.
like this:
(...)
# copy properties over to new instance
cp "$OldServerDir"/*.properties $NewServerDir"/
cp "$OldServerDir"/.idpass $NewServerDir"/
(...)NB: If anybody is interested I'll be happy to share the complete update script.