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This may depend on the cause of those "holes."

If they are caused by wear, that MAY (or maybe not) mean that the lower
teeth have been occluding so long and so hard that some spots are now
worn all the way through the denture base.

If that is the case, then your vertical dimension of occlusion may be
decreased from what it was when the upper denture was new.

If (and this is a very big IF, as I can't see your occlusion on the
net) your centric occlusion now involves actual contact between the
incisal edges of the lower teeth and the upper palatal soft tissue,
then any repair that adds thickness to the worn holes would cause
premature occlusal contacts at the thickened-repair locations.

That could throw off the rest of your occlusion.

A reline can often be done instead of a new denture. A reline often can
retain the current occlusal pattern by increasing the vertical
dimension evenly over the whole denture. Such a reline fills any holes
caused by wear.

Of course, if the holes are NOT caused by occlusal wear, and if your
current closed-centric bite does NOT have contact through those holes
of the lower teeth and the upper palate, then my discussion here simply
doesn't apply!

(It would be so much easier if patients could be examined by Internet
magic!)

Best regards,
- dentaldoc