I’ve moved this to feature request. In today’s 2.6.2 beta build we’ve added an option to allow you to force the metadata matching method. You now have 3 options to choose from under Conversion task → Expert settings → Metadata corrections:
- Episode name
- Season/Episode no
- Original air date
In your case you can choose Season/episode no and it should fix your issue where you have the same episode name across multiple seasons.
Let me know how it goes.