i have one problem the sshd_config sometime looks like this

#Port 22
Port 4444
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After we modify the file with above code it becomes like this

Port 4444
Port 4444
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Right, that's what your code in the OP does, and that's what I mentioned in my third "bullet" paragraph as probably being a bug.

Now, you seem to be saying that you simply want to delete all commented lines (the ones beginning with "#"), which is easy enough to do:

while (<SSHD_CONFIG>) {
    next if ( /^#/ );
    s/^port.+/Port $sshport/i;
    print SSHD_CONFIG_NEW;
}
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But some people prefer to leave the comment lines in, because sometimes these lines hold important information that might be useful someday (e.g. documentation, or details about a prior or alternative configuration that might be needed when conditions change).

That's why the version in my first reply used the parens and the "$1" in the s/// statement, to preserve the "#" character while changing the port number. Actually, I think it may be best to retain the comment lines unchanged, and only edit the "uncommented" line -- this also turns out to be the simplest method:

while (<SSHD_CONFIG>) {
    s/^port.+/Port $sshport/i;
    print SSHD_CONFIG_NEW;
}
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