I updated my site name to include https from http and while 99% of the code is ok when I view page source I see the an Item that I think is causing the alert issue as it has http in it.
The external solution is to Show Contents of the specific theme (Themes, then right-click to Show Contents), and then physically alter the address on the HTML file.
The internal solution, however, could be mitigated by JavaScript in RapidWeaver.
Under Inspector > HTML > JavaScript:
This snippet will find any script containing the specified address, then replace it with the new one. If you intend on indefinitely deferring it, you can substitute ‘attr()’ for ‘remove()’.