What I do is simply add a TODO statement. It does not flag the resource, but the doc keyword TODO does show up in Git and as marks in the gutter. Hopefully those warnings will be enough to keep you and others from using it.
But not always. As we know, @Deprecated is essentially a stop-gap until something is really removed for good and the code is cleaned up properly.
Here's an example of a shape.xml file that I no longer use (and want to @Deprecate).
<?xml version="1.0" encoding="utf-8"?>
<!--
Border around card elements. For now this is used only within the
cards of the Questionnaire RecyclerView.
TODO: This file is obsolete. Use CardView instead.
-->
<shape
xmlns:android="http://schemas.android.com/apk/res/android"
android:shape="rectangle" >
<stroke
android:width="@dimen/tiny_card_margin"
android:color="@color/colorPrimaryDark" />
<solid
android:color="@android:color/white" />
<corners
android:radius="4dp" />
</shape>