Well, it's really all one in the same . . but it depends on how far the original holes were drilled into the core, because the plug is going to have a different density than the core, and essentially changes the core shape, thus changing the core specs.  So basically, the same ball drilled the same way will react slightly differently between a fresh drill and a plug and redrill. 

I just bought an 811a se that is pin up and was thinking about moving to pin down?

I don't think that would hurt anything, other than the plug from the first layout possibly being in your track.