I have no idea what $bFlush is, what it means by "specified", what it means by "and a true value", or what RegFlushKey() is and why it would be necessary.
If you call Flush like this $Registry->Flush; or this $Registry->Flush();, then you are not "specifying" a value. Otherwise you are. If you do pass a value, it is false if it is undefined, 0, "0", or "" (the empty string). Pretty much anything else is true

RegFlushKey is a Windows API subroutine. See regflushkey.

This doesn't give me an error, but it doesn't work:
$Registry->Flush();
How do you know it didn't work? I don't understand what you mean when you say above "Both keys are being deleted, but the result is similar to what would happen if I deleted the second key first and the first key second."

So, I tried this:
$Registry->Flush( $bFlush );
and I get this error:
Usage: $Key->Flush( $bFlush );
This looks like a bug in Win32::TieRegistry. I think this
my( $flush )= @_; @_ and croak "Usage: \$key->Flush( \$bFlush );";
should be
my( $flush )= shift(@_(; @_ and croak "Usage: \$key->Flush( \$bFlush );";

In reply to Re: TieRegistry - How does Flush( $bFlush ) work? by Thelonius
in thread TieRegistry - How does Flush( $bFlush ) work? by trout16

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