If you have a public extension that you would like that we add in the JMS definition, you can send us the extension in the attachement of an email.
Otherwise, any update that we will do will overwrite you specific modification.
If you have a specific extension, we can also create a specific plugin to let you add in the future other specific definition and sharing.
If you want that we create the plugin for you, this is possible with our billable support and we can do that in 1 hour.
www.jms2win.com/en/joomla-multisite?page...35&category_id=1
Concerning the update/upgrade of the schema in each website, you need to go in the back-end of the slave site to perform the extension manager / database => fix
or perhaps the update menu.
Today, there is no propagation processing to perform the database upgrade automatically in each slave site attached to the standard joomla database fix.
I will cross-check the processing with the maintenance menu to verify the schema update.
The fact that the version number disappear in the slave site seems to be due to the fact that no rule were selected to verify the extension or that no rule were found.
In the next release of JMS 1.3.30, I have added a cross-check to verify that we found the new version number before applying the change in the schema table.