MOdify the pad in question to have a pads smaller then the drill and select non plated
I have actually done that. I have my correct pad on the "opposite" layer and have set the pad size on the "Mounted" layer to 0. However, if I choose "non-plated" I get Connectivity issues when running the design checks as it is expecting routes to both layers. With plating, there are no connectivity issues as it treats both layers as connected, however I don't want the holes to be plated. I need a way to tell Pads that the component is "single sided" so I don't have a slew of design check errors.
Fills also attempt to join on both layers so I have copper going right up to the holes on the wrong layer. I would like that hole to be treated as a drill or something similar on the layer with "no connection". I added a keepout to the decal to keep the copper away from the drill that but it is not an elegant way of doing it.
I am using Pads Layout VX.0
In this case for one pin of the component you will have to ignore missing connection due to the non-plated hole. In two or multi layer designs system consider every through pin as plated and if it is missing, reporting connectivity issue. If the design were a single sided board, PADS can deal with the none plated pins by declaring in Layer Definition that it is a single sided design.