Although it might not be documented, using the plesk command line tools one can turn on and off the legacy option "Separate SSL and non-SSL content".
I got stuck with that option after migrating around 400 sited from plesk 9.5.4 to a brand new installation of plesk 10.4.4, and that compatibility message appeared in all domain options. Clicking the plesk GUI for each domain was too much... so I searched through the migration logs and found during the domain migration, there is a command line option that sets all sorts of options, one of them being -same_ssl false; so, by setting that option to true the message disappears...
In my linux system the command I executed was
/opt/psa/bin/subscription --update domain_tld -php true -php_handler_type module -ssl false -same_ssl true;
You can accomplish the same thing by changing the 'Use a single directory for housing SSL and non-SSL content' option before migrating the plesk 9.5.4 domains. So login into the old plesk server and follow these steps:
Plesk
-> Domains
-> select the check-boxes of the domains you want to change
-> click 'Modify'
-> in the field 'Use a single directory for housing SSL and non-SSL content' select 'Switch on'
-> press 'OK'
-> Domains
-> select the check-boxes of the domains you want to change
-> click 'Modify'
-> in the field 'Use a single directory for housing SSL and non-SSL content' select 'Switch on'
-> press 'OK'
that's it
