diff --git a/libbuild2-autoconf/libbuild2/autoconf/rule.cxx b/libbuild2-autoconf/libbuild2/autoconf/rule.cxx
index a4efd15..d847006 100644
--- a/libbuild2-autoconf/libbuild2/autoconf/rule.cxx
+++ b/libbuild2-autoconf/libbuild2/autoconf/rule.cxx
@@ -110,6 +110,15 @@ namespace build2
       // checks by in::rule.
     }
 
+    void rule::
+    perform_update_pre (action, const target& t, ofdstream&, const char*) const
+    {
+      // Clear the checks set which may have already been partially populated
+      // during depdb verification.
+      //
+      t.data<match_data> ().checks.clear ();
+    }
+
     void rule::
     process (const location& l,
              action a, const target& t,
diff --git a/libbuild2-autoconf/libbuild2/autoconf/rule.hxx b/libbuild2-autoconf/libbuild2/autoconf/rule.hxx
index 91877b3..d9b30a9 100644
--- a/libbuild2-autoconf/libbuild2/autoconf/rule.hxx
+++ b/libbuild2-autoconf/libbuild2/autoconf/rule.hxx
@@ -27,6 +27,10 @@ namespace build2
       virtual void
       perform_update_depdb (action, const target&, depdb&) const override;
 
+      virtual void
+      perform_update_pre (action, const target&,
+                          ofdstream&, const char*) const override;
+
       virtual void
       process (const location&,
                action, const target&,