I've done this in the past and it has worked perfectly, however in DNN 5.6.3 I've come across and issue where when I place a call to execute a JS script in place inside the Text/HTML editor, the JS script not only does not function but also completely disappears when i go back to it.

Here is an example:

Create simple alert and call it "myscript.js" place the path of it inside your TEXT/HTML FCK Editor on the HTML CODE SIDE so that it reads /Portals/0/myscript.js or you can place the entire path of http://www.mydomain.com/Portals/0/myscript.js on the HTML CODE Side of the FCK editor.

Hit Save and see if your code functions.
ISSUE:
1)You will find that the code will not function.
2)When you go back into the FCK Editor, you will find that DNN has removed the entire scirpt and path. This happens even if you place the script within div or table tags... the FCK HTML Code is striped out.

QUESTION:
What is a work-a-round for this issue to call a JS script in place inside a text/html editor on the CODE Side?
NOTE: Upgrading to DNN 6.X is not an option at this time.

Please advise.
Thanks