diff --git a/merge-ort.c b/merge-ort.c
index 6eac0cef49..bd237f3472 100644
--- a/merge-ort.c
+++ b/merge-ort.c
@@ -253,10 +253,11 @@ static void free_strmap_strings(struct strmap *map)
 	}
 }
 
-static void clear_internal_opts(struct merge_options_internal *opti,
-				int reinitialize)
+static void clear_or_reinit_internal_opts(struct merge_options_internal *opti,
+					  int reinitialize)
 {
-	assert(!reinitialize);
+	void (*strmap_func)(struct strmap *, int) =
+		reinitialize ? strmap_partial_clear : strmap_clear;
 
 	/*
 	 * We marked opti->paths with strdup_strings = 0, so that we
@@ -266,14 +267,14 @@ static void clear_internal_opts(struct merge_options_internal *opti,
 	 * to deallocate them.
 	 */
 	free_strmap_strings(&opti->paths);
-	strmap_clear(&opti->paths, 1);
+	strmap_func(&opti->paths, 1);
 
 	/*
 	 * All keys and values in opti->conflicted are a subset of those in
 	 * opti->paths.  We don't want to deallocate anything twice, so we
 	 * don't free the keys and we pass 0 for free_values.
 	 */
-	strmap_clear(&opti->conflicted, 0);
+	strmap_func(&opti->conflicted, 0);
 
 	/*
 	 * opti->paths_to_free is similar to opti->paths; we created it with
@@ -1344,7 +1345,7 @@ void merge_finalize(struct merge_options *opt,
 
 	assert(opt->priv == NULL);
 
-	clear_internal_opts(opti, 0);
+	clear_or_reinit_internal_opts(opti, 0);
 	FREE_AND_NULL(opti);
 }