GoDaddy doesn’t support Let’s Encrypt by itself. So how did you obtain your first certificate? According to them you have to repeat that process for all your subdomains.
The best guide I’ve seen for using Let’s Encrypt with GoDaddy’s CPanel-based hosting is here. It requires using the Linux/SSH shell but that enables it to perform automatic renewal so you don’t have to manually deal with it every three months when your certificates expire.
Unfortunately, I don’t use GoDaddy, so I can’t be of much help. 
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