nnml group has move messages than gnus sees

[Harry Putnam <reader@newsguy.com>]

I should know how to do this and seem to recall having done it at some
time in the past.  That is:

Make gnus `see' messages in a (nnml) group that are not showing up by
normal means.

Gnus `sees' 1459 messages in nnml:all

ls sees 6409 in ~/Mail/all

I ran 
M-x: nnml-generate-nov-databases-directory <RET>  ~/Mail/all <RET>

But message count stayed at 1459.

I tried rm Mail/all/.overview

Then nnml-generate-nov-databases-directory

Still no change in count.

So, how to make gnus `see' the other 4500 or so messages?

These messages have been moved around a bit.  I rsynced my whole mail
setup from one machine to another a while back but saw no errors or
etc.

However, it may be the case that I am just now noticing the anomally
and it has been there ever since the move.

But in general, how would one go about forcing gnus to recognize the
missing messages?