Ryan, thanks for the response. Are you aware if this changed recently? I am 98% certain we worked with the same project day in and day out and just checked in the data at the end of the day.
Just now I exported a feature class to ArcPad and went out and shot a point. Checked it in. Fine. Then I went to check it out again and I cannot use the same as the project before "a folder with that name already exists" This means when we check-out we have to either delete the folder to re-export or export with a new name and I am 100% sure that we didn't do that before. I had it rather streamlined so it was bring in the GeoXH, dock it, let it sync, open ArcMap, check-in, done. And we would just repeat that part of the process the next day.