The CGI part looks correct. One problem is that you are reading the file line by line. If it is binary file, you want to read it all in one go. Make sure to check that the content-length is valid and you read the full length. Either read or brackets with $/ undefined will work.

read $fh, $contents, $length;
$/ = undef;
$contents = <$fh>;
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The way to debug the problem is check that the file is valid at various stages of process. Check the file before upload, check the temporary file, check the contents read into memory, check the value in the database.