If domains were migrated with Plesk migration tool (you clicked Tools & settings > Migration and Trasfer), then they run in legacy mode of separated folders for SSL and non-SSL. If you wish to change that
1) go Domain > Hosting Settings > uncheck "Run the website in compatibility mode for the legacy option "Separate SSL and non-SSL content"
2) or call "plesk bin domain -u domain.com -same_ssl false" in CLI
Simple script can do #2 for all your domains
If you are not familiar with CLI and scripting, you will need to perform #1 for each domain manually
Regards