$b = 0;
$_ = q(aaa; ; bbb ; "ccc ; ddd ;"  ee;e  ";"  fff ;);
$a = join '', map {$b =!$b if /"/; s/;/'&&'/ unless $b; $_} split //;

output:
aaa&& && bbb && "ccc ; ddd ;"  ee&&e  ";"  fff &&