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my $bufflen = 4 * 1024; #or w/e

...
    $result = read ( IN, $buffer, 
            $bufflen-length($buffer), length($buffer) );
} while ( $result && ( length($buffer) < $bufflen ) );

my $newline = "\n"; #or some other unique record separator

...

## this is important: prefix the remainder before next chunk
$buffer = $remainder;

$buffer .= <IN>;

foreach my $regex (@conversions) {
    my @results = ( $buffer =~ s/$regex->{from}/$regex->{to}/g );
...
}
## and do whatever with the result
print OUT $buffer;