Hi,
since all my years in Innovator I never was forced to use this file. Normally there is always a way to avoid these kind of queries.
According to the xml, you have to create a copy of this template.
I assume you have to but your custom query into the <whereAttribute> tag inside CDATA:
<whereAttribute>
<!-- Add a suppression for Item "where" attribute. NOTE: it uses both @Parameter and @ParametersList -->
<template><![CDATA[
[Part BOM].related_id=(select id FROM innovator.Part WHERE ITEM_NUMBER='424-01-00001' and IS_CURRENT='1')
]]></template>
</whereAttribute>
Maybe this is already enough to make your AML query work.