Here's another approach:

my @orig = ($/, $\);
undef($/);
undef($\);
open (JE, $file) || die "Cannot open $file";
(my $j = <JE>) =~ s/orig/new/g;
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At this point you can either:

close (JE);
open (JE, "> $file);
print JE $j;
close (JE);
($/, $\) = @orig;
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or, more efficiently:

seek (JE, 0, 0);
print JE $j;
close (JE);
($/, $\) = @orig;
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