Your initial question was about the UNA upgrade. The mentioend commands from the install/sql/disable.sql file of every module relates to the situation when you need to "restore the basic settings" of the app. This is another case and yes, this procedure deletes all page blocks, menu items and settings of the app.

So the best way to customize pages - do eveything via the Studio and make regular backup of the files and database, for example twice on month.