diff --git a/Lib/fontTools/merge.py b/Lib/fontTools/merge.py
index 203b3cd8e..2cc4d6234 100644
--- a/Lib/fontTools/merge.py
+++ b/Lib/fontTools/merge.py
@@ -771,7 +771,10 @@ def merge(self, m, tables):
 	assert len(tables) == len(m.duplicateGlyphsPerFont)
 	for i,(table,dups) in enumerate(zip(tables, m.duplicateGlyphsPerFont)):
 		if not dups: continue
-		assert (table is not None and table is not NotImplemented), "Have duplicates to resolve for font %d but no GSUB: %s" % (i + 1, dups)
+		if table is None or table is NotImplemented:
+			log.warning("Have non-identical duplicates to resolve for font %d but no GSUB. Are duplicates intended?: %s" % (i + 1, dups))
+			continue
+
 		synthFeature = None
 		synthLookup = None
 		for script in table.table.ScriptList.ScriptRecord: