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.php file:

define('BX_FORCE_AUTOUPDATE_MAX_CHANGED_FILES_PERCENT', 0.05);

to:

define('BX_FORCE_AUTOUPDATE_MAX_CHANGED_FILES_PERCENT', 1.00);

Then try to upgrade UNA or modules as usual.