You might get a better error message by trying to open a file: 
open my $handle, '<', $file or die $!;

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There are configurations where root isn't allowed to view some directories (for example with selinux) where -e would return false. But that's pure speculation on my side.

In reply to Re: Wrong file check while running using sudo by moritz
in thread Wrong file check while running using sudo by accessdenied

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