If $file is your filename:
$file
my $file = '=Web_Help_Desk_Pro%26Lite.pdf';$file =~ s/%[0-9a-f]{2}//gi;
i.e. replace % followed by two hex characters with the empty string.
%
To just remove the percent sign and the following two hex digits:
$path =~ s/%[\da-f][\da-f]//gi;
This should work
sed 's/%[[:alnum:]]\{2\}//g' INPUT_FILE