A quick update for all who are looking for resolution as I am…
I just got a reply from a Partner Support Specialist in response to the Shopify Partner Support chat I started last week. She told me they’ve checked my app for deprecated calls and found that there had not been any deprecated calls for over 5 months, so she is not sure why I have received the warning email from the team. She also expressed that she is reaching out to the internal team to discuss this and find out what she can for me.
Hopefully will hear something helpful soon.