Well, you have to change code that uses $r->args to parse the query string because that doesn't work anymore. See the porting doc for more info. You can set the complete query string with $r->args(), which might allow later code to see your parameter changes, or you might be able to use Apache2::Request and modify the params using the APR::Table API on the object it returns when you call it like this:

my $table = $req->param;
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I'm not sure those changes are visible to anyone else though.