I struggled with this for awhile because sometimes you have rewritten URLs that you want to pass a query string but most of the info and examples do not support this.
Take a typical example like this:
RewriteRule ^(.*)-(.*)-(.*) /?module=$3&id=$2
You need to add the QSA flag to make it work like below:
RewriteRule ^(.*)-(.*)-(.*) /?module=$3&id=$2 [QSA]
The QSA preserves the original query string but also appends it wit........