|Is there any explanation for that?
One explanation is that $file2 exists, but it wasn't created where you expected and you're looking in the wrong place for it.
You can use File::Spec to determine the absolute path of $file2 - untested:
my $file2 = 'whatever it is';
my $abs_path = File::Spec->rel2abs($file2);
print $abs_path, "\n";
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