That was tough to wade through, you should put code in-between <code>...</code> tags. But basically, I see this

my $filePath1 = "/tools/busapps/LAMP/dev/APP/htdocs/APP/APP_Attachment
+s/2016/LGop.pdf";
open (my $upload_filehandle,'<',$filePath1);
binmode $upload_filehandle;
my $filecontents;
{ local $/ = undef;
$filecontents = <$upload_filehandle>;
} 
my $fContent = decode_base64( $filecontents );
[download]

and unless your file naming conventions are strange, a pdf file is not base64 encoded.

What you need to do is first identify and isolate a file that is failing to decode. Move it off to the side and then write a very small script that just opens that problem file and tries to decode_base64 it. More than likely, you'll find the problem is with the actual file (it's not base64 encoded) and not the decode_base64 routine.