use Prompt::Timeout;
use constant TIMEOUT => 5;

...

if (defined($size_remote))
{
    my $default = ($size_remote == $size_local) ? 'N' : 'Y';
    my $answer  =  prompt('Overwrite?', $default, TIMEOUT);
    
    upload($_) if $answer =~ /^Y/i;    # overwrite
}
else
{
    upload($_);
}