The best method to set operators for multiple airports has always been using the rules_handling file.
And, you should not edit the rules file in the Addon Manager\Texture folder but, instead, make a custom version in %APPDATA%\Virtuali\Texture, otherwise every Live Update would revert your changes to default, that's why there's an extra set of files you can edit in %APPDATA%, which have an higher priority over the stock ones.
If your custom rules specify, for example, a list of airports for an operator, check if that ICAO code it's in use by another operator too, because depending on the case, you might want to either keep it or remove it.