That should not be an issue. You should just make your change and add a filter option that will do the trick.
The filter.xml consists of a set of filter elements, each with a mandatory root attribute and an optional list of include and exclude child elements. The include and exclude elements can be added as optional children to the filter element to allow more fine grained filtering of the subtree during import and export.
define something like this
<workspaceFilter version="1.0">
<filter root="/apps/project1" />
<filter root="/etc/project1">
<exclude pattern=".*\.gif" />
<include pattern="/etc/project1/static(/.*)?" />
</filter>
<filter root="/conf/*" />
</workspaceFilter>
You should refer this for more details on filter.xml
https://jackrabbit.apache.org/filevault/filter.html