Semantically you are composing a new value for the variable; why not write the code that way as well?

$time = "$1:$2:$3.$4"
    if $time =~ /^(\d{2})(\d{2})(\d{2})\.(\d{2})/;
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This also makes it easier to yell if the data didn't conform to expectations:

if($time =~ /^(\d{2})(\d{2})(\d{2})\.(\d{2})/) {
    $time = "$1:$2:$3.$4";
}
else {
    die "Malformed time: $time\n";
}
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