Exactly!  When I removed the cover sills from my project MK1, the
remains of the previous cover sills(!) we just flakes of rust.  I
didn't even find any of the original sills at all!

I agree with Keith.

If you haven't already, pull up the carpets and check the condition of
the interior floor. Has it been repainted properly? The usual bodge is
to put undercoating over the area where the paint was burned off. It
should have been primed and well painted.

From the outside of the car, count the number of layers of metal in
the horizontal seam below the door jam. There should be two layers. If
there are three this means that the repair on your car was done
without removing the original rusted sill. This leaves rusted metal
inside the sill box section to continue rusting. This will spread
fairly quickly to the new metal. I have seen cars imported to the
U.S., at great expense, that have had as many as 5 layers.

If either of the above appear to be the case, I would try to get my
money back and have someone better do the repair. This is a difficult
decision because of the money involved. However, there is no doubt in
my mind that the over-sill must be removed and the repair done right.
There is no reason removing the over-sill should damage the floor,
other than the fact that person doing the removal is incompetent.

Cheers,

Kelley