Oh, silly me! I finally see the problem, we both were talking about different options, I'm sorry.
When you upgrade to 10.4.4, your subdomain will get its own DNS zone, so A records will be created in subdomain zone, and consequently will be deleted from main domain zone
I think there will be no problem with the upgrade, but you should write down all subdomain records like "shop" CNAME so you are able to create them again in the new DNS zone that will be created for your subdomain.
I hope I made myself clear this time.