You might want to try the 's' modifier on your regex

$line =~ s/wordone\s*\((.*)\)\;//wordtwo\:$1\;/s
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And also not have b0rken regex in the first place

$line =~ s/wordone\s*\((.*)\);/wordtwo:$1;/s;
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You're escaping characters that don't need to be escaped (i.e non-alphanumeric non-meta-characters <pant> <pant> ;).
HTH

broquaint