Sorry I assumed you were using the Remove Query Strings plugin. Is it a feature of WProcket?
I am 100% certain that the issue is not with the theme as removing query strings will have no affect on how the theme works.
Look at the source code of your site, removing query strings simply changes the links of things like the stylesheets from this:
/wp-content/themes/trusted-pro/style.css?ver=4.9.4
to this:
/wp-content/themes/trusted-pro/style.css
This will have no affect on the theme displaying things like the featured services and headline etc.