I think XSLT, or Extensible Stylesheet Language and Transformation, might be that tool that you need.
It's been a while since I last used XSLT, but essentially what you would do is to make a template that will match the CDATA node and then output an empty node. Something like this (not guaranteed to work, I haven't run it myself):
<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet xmlns:xsl="w3.org/1999/XSL/Transform" xmlns:gravitDesigner="ns.gravit.io" version="1.0">
<xsl:output method="xml" indent="yes"/>
<xsl:template match="//gravitDesigner:gravitGraphicSource/text()">
<xsl:comment>Data removed</xsl:comment>
</xsl:template>
</xsl:stylesheet>