PhpStorm - new lines (linefeed) are being removed when saving to remote server

Using PhpStorm 2017.1.4

I have a MySQL query string in PHP:

<php

    $MySQL_Query_String = "SELECT * 
    FROM  `VISITOR` 
    WHERE  `ID` =3

    -- eventually add the date order here as well
    ORDER BY `VISITOR`.`INACTIVE` ASC, `VISITOR`.`NAME` ASC";

?>

I left a comment to remind myself of something with the -- to ignore that comment.

When I run this code in the browser - then this part is not being run by MySQL:

ORDER BY `VISITOR`.`INACTIVE` ASC, `VISITOR`.`NAME` ASC

When I debug - I see that the string is being concatenated and sent like this:

MySQL_Query_String = "SELECT * FROM  `VISITOR` WHERE  `ID` =3 -- eventually add the date order here as well ORDER BY `VISITOR`.`INACTIVE` ASC, `VISITOR`.`NAME` ASC";

The line return feeds are missing. The last line is now being ignored by MySQL.

The funny thing is - I have this exact same code in another application - using the same version of PhpStorm - and it does NOT remove the line feeds like the one mentioned here.

As far as I can tell - and I have copied both back and forth from each application - there is no difference.

I lost a number of hours debugging this. I did not immediately see that the lines returns were being ignored.

Why is PhpStorm removing the line feeds here?