Dear Phil,  No doubt you will get lots of replies, but if you don't,
I think the holes to which you refer are known as "nodal holes" and
serve to cause the pipe to speak one octave above its length.

To make that clear, what I mean is if you take an 8' pipe, for example
and blow it, it gives bottom C on an organ keyboard.  If you drill a
small hole about 4' from the mouth of the pipe, it will now play the
octave above.  Such a rank of  pipes is called a "Harmonic rank"
because the pipe (and others in the same rank) are sounding what is
called the first harmonic.

I have not dealt with the type of instrument you are talking about,
so I may be wrong.   If these _are_ indeed nodal holes, they should
_not_ be covered.   An organ builder will give you more information.

Paul Morris