Where is the SQL Assistant option to open all .sql files in a new instance of SQL Assistant? I'm having no luck finding that check box in Tools > Options.
There is no option within the application to open new files in a new instance of the app.
There is an option to open new files in a New Query Tab.
However it will only create a new tab if you have changed the text in the current tab since it was last loaded, saved, or executed.
If you double click an '*.sql' file in Windows Explorer (or from the Start menu) that file will be opened in a new instance of SQL Assistant.