You're looping more than you mean to. I think you want to pare your code down to just:
my $flag = 0;
local ($^I, @ARGV) = (".bak", "/var/ww/htdocs/cgi-bin/user.txt");
while (<>) {
$flag = 1 if !$flag and s/\|No$/|Yes/;
print;
}
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