The | is the "or" operator in a regular expression. You need to escape it for your regex to work:

s/\|\|/|\\N|/g;
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if I use

s/\|\|/|\\N|/g;

it replaces || with ||. The \N seems to be an invisible newline character, and I want it to just be '\N'.

I suspect your problem is that you are writing back to the filehandle IN when you (presumably) only opened it for read.

open( IN, '<', $filename ); # input
open( OUT, '>', 'newfilename.txt' ); # output
while ( <IN> ) {
    s/\|\|/|\\N|/g;
    print OUT;
}
close IN;
close OUT;
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--
meraxes

\n will result in a newline.
\N will result in a syntax error.
\\N will give \N.

If you're not getting \N from \\N, there's something you haven't showed us.

Update: meraxes caught the problem.

Because | is a special character to regular expressions (which the left hand side of a substitution is). Read quotemeta (and probably perlretut and perlre as they also cover this).

| is a special character for regexs. It needs to be escaped.

s/\|\|/|\\N|/;
[download]

However, that solution is far from complete.
What if the first field is empty?
What if the last field is empty?
What if there's more than one empty fields?
What if there's more than one empty fields in a row?
Fix:

s/\|(?=\|)/|\\N/g;
s/^\|/\\N|/;
s/\|$/|\\N/;
[download]

As a one-liner:

perl -pe"s/\|(?=\|)/|\\N/g; s/^\|/\\N|/; s/\|$/|\\N/" infile >outfile
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if I use

s/\|(?=\|)/|\\N/g; s/^\|/\\N|/; s/\|$/|\\N/g;

it replaces || with ||. The \N seems to be an invisible newline character, and I want it to just be '\N'.