well... \L lowercases everything after it... \l just does the first letter... use either \L or lc(). I suppose for the filehandle you could do...

$line =~ s/([A-Z]{4,})/___$1___/g;
$line = lc($line);
$line =~ s/___([a-z]{4,})___/uc($1)/ge;
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that would work... there are probably better ways, but I'm still asleep... you don't need a regexp for the lc conversion, just running it through lc() should be fine, as I showed.
                - Ant