Following this answer:
cat xquery.txt
declare namespace w = "http://schemas.openxmlformats.org/wordprocessingml/2006/main";
copy $input := doc("/tmp/file.xml")
modify delete node $input//w:rPr
return $input
Input file
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<root xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main">
<w:lvl w:ilvl="0">
<w:rPr>
TO REMOVE
</w:rPr>
<w:rPx>
<w:rFonts w:ascii="Symbol" w:hAnsi="Symbol" w:hint="default"/>
</w:rPx>
</w:lvl>
</root>
$ java -cp "/path/to/lib/saxon-he-11.4.jar" net.sf.saxon.Query -qversion:3.1 -q:xquery.txt
Exception in thread "main" java.lang.NoClassDefFoundError: org/xmlresolver/Resolver
at net.sf.saxon.lib.CatalogResourceResolver.<init>(CatalogResourceResolver.java:46)
at net.sf.saxon.Configuration.init(Configuration.java:367)
at net.sf.saxon.Configuration.<init>(Configuration.java:230)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at java.base/java.lang.Class.newInstance(Class.java:584)
at net.sf.saxon.Configuration.newConfiguration(Configuration.java:246)
at net.sf.saxon.Query.doQuery(Query.java:265)
at net.sf.saxon.Query.main(Query.java:103)
Caused by: java.lang.ClassNotFoundException: org.xmlresolver.Resolver
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
... 11 more
From doc
-q:input
Another try with an older version:
$ java -cp "/path/to/lib/saxon9he.jar" net.sf.saxon.Query -qversion:3.0 -q:xquery.txt
Error on line 2 column 1 of xquery.txt:
XPST0003 XQuery syntax error near #...rocessingml/2006/main"; copy $#:
Unexpected token "copy" in path expression
Static error(s) in query
Based on the Saxon Home Edition (HE) documentation, it supports just the XQuery 3.1 Minimal Conformance. And it doesn't include the following:
Optional features not provided: XQuery 3.1 Schema Aware, XQuery 3.1 Typed Data, XQuery 3.1 Static Typing, XQuery Update 1.0
And you need XQuery Update support for your task.
It seems that you would need to use Saxon PE or EE editions for your objectives.
For the reference: Product Description for SaxonJ-HE (Home Edition)