When you update base you end up updating all installed modules. I suggest that any changes you make to screens etc are done as a module rather than on the system - typically for our customers we create a views module which holds these sorts of customisations.

Extra details: There is a module (App) that is called "base". Every other module in Odoo depends on this one. You will need to clear the Apps filter to find it and be in Developer mode to verify (there are a few that have base in the name). Upgrading a module recreates and resets all XML created records from the module. Since all modules depend on base this has the effect of recreating every XML record defined in every module. Any records created by XML that were deleted or edited will be reset. This "fixes" common issues that occur when users delete things or edit Views or Menus or Window Actions etc that cause Odoo to not work correctly.