2 things actually....

Studio > Settings > System > Site Settings > Force auto-update, even if some files were modified
it will make updates to work if less than 5% of files are modified.

and then do this:

if more than 5% of files are modified is to overwrite any changes you've made in source code, then you need to change the following line in inc/classes/BxDolInstallerUtils.phpfile:

define('BX_FORCE_AUTOUPDATE_MAX_CHANGED_FILES_PERCENT', 0.05);

to:

define('BX_FORCE_AUTOUPDATE_MAX_CHANGED_FILES_PERCENT', 1.00);