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$s = "Bla (bar;) bla bla; bla bla (foo; bar); bla bla 
Bla bla bla; bla bla (foo; bar); bla bla 
Bla bla bla; bla bla (foo; bar); bla bla 
Bla bla (bar;foo;bar) bla; bla bla (foo; bar); bla bla 
Bla bla bla; bla bla (foo; bar); bla bla
";

 s/            # search for...
 \(            # a literal "("
 (             # begin storing what follows (in "$1")
...
 )             # stop storing in "$2"
 \)              # a literal ")"
 /($1,$2)/gx;        # and replace all that with...see below...