Well, function Encode::encode takes third argument that allows to define handling for "bad" characters. I believe, with the help of that one can replace them with other than question mark (?). For example

use strict;

use Encode;

# my raw data
my $data = "\xe0\xe1\x02\n";
# interpret it as text in encoding CP1251
my $txt = Encode::decode("cp1251", $data);

# convert text to octets in encoding Latin1.
# Replace bad ones with X
my $nd = Encode::encode("latin1", $txt, sub{ return "X" });

# just to see the result in the terminal which uses UTF-8 encoding
Encode::from_to($nd, "latin1", "UTF-8");
print $nd, "\n"
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