This worked for me.
Parse.xml contained records which had the &.
<row>
<field column="NAME2">FY13 O&amp;M - BNLER</field>
</row>
<row>
<field column="NAME2">FY12 RDT&amp;E - Pharmacy</field>
</row>
Added this namespace xmlns:util="jelly:util" to the gel:script tag.
<util:loadText file="Parse.xml" var="ToClean" />
<util:replace old=";amp;" new=";" var="Cleaned" value="${ToClean}"/>>
<core:new className="java.io.PrintWriter" var="PrintOne">
<core:arg type="java.lang.String" value="Cleaned.xml" />
<core:arg type="java.lang.String" value="UTF-8" />
</core:new>
<core:invoke method="print" on="${PrintOne}">
<core:arg value="${Cleaned}" />
</core:invoke>
<!-- Close the file -->
<core:invoke method="close" on="${PrintOne}" />
After the replace Cleaned.xml contained:
<row>
<field column="NAME2">FY13 O&M - BNLER</field>
</row>
<row>
<field column="NAME2">FY12 RDT&E - Pharmacy</field>
</row>