Hi @DStahl,
Thank you for reaching out to the Community!
I found this solution from @Jnix284 for you on a similar post “Auto-reply emails not threading, creating new tickets/conversations” that might help you!
I also wanted to invite a couple of subject matter experts to this conversation @HFisher7, @danmoyle and @Jnix284, do you have any other workaround or tips to help @DStahl, please?
If anybody else has anything to add and/or share, please feel free to join in the conversation 
Thanks and have a lovely day!
Best,
Bérangère