Redirect shop.mywebsite.com to mywebsite.com/shop

1. In GSC, add the shop subdomain as a profile and make sure there is a profile for the main domain too. Give the new profile(s) a day or two to get situated.

2. If you haven't already, pick either www or non-www for your main site and make sure the URLs with the one redirect to the URLs of the other. Here's how to do with Apache for instance: https://www.siteground.com/kb/how_to_redirect_www_urls_to_nonwww/ . Also, here's an explanation for why choosing one is important: https://www.spyfu.com/blog/www-vs-non-www/

3. Design the redirect mapping (https://support.google.com/webmasters/answer/6033086) and then set up the 301 redirects from the shop subdomain to their new counterpart pages on the main domain. Here's a guide about Shopify redirects: https://help.shopify.com/en/manual/online-store/legacy/menus-and-links/url-redirect .

4. Once the 301s are done, then do a change of address from the subdomain profile to the main domain profile via search.google.com/search-console/settings/change-address .

The 301's will help redirect referral traffic immediately and the change of address in GSC will help Google understand that the shop domain is no more (along with all of the redirects too) and update domain and entity-related data involved with your existing rankings. I think that's everything since you're set with SSLs and whatnot.