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There are settings like BackendCSSFileList that can be changed at the 3 settings/override, extension/settings and settings/siteaccess levels.
However, take ezfind.ini
There are settings like RawFilterList that CANNOT be overriden at the siteaccess level.
There is ONLY an extension/settings (peer / entire site) and settings/override
The alternative is to comment OUT the extension/settings like #RawFilterList
and thus allow a siteaccess to re-initialize, but this is NOT ideal becuase then EVERY siteaccess must have it.
PLEASE, identify ini files within an extension that do NOT have .append.php and consider then the same level as the default settings/*.ini default files.
This would preserve the 3 levels of override using extensions INI files.
Try and override an extension/settings INI value with a siteaccess... you cannot because an extension setting take precidence over a siteaccess one.