Grey --
I'm pretty sure that once ArcSWAT selects the HRUs that fulfill the threshold requirements, it then calculates the percent area of each HRU in the selected set, and applies that percentage to the total subbasin area to get a new HRU area. In other words, each of the selected HRUs expand a little bit, proportionally, to fill out the entire subbasin area, compensating for the loss of area from the excluded potential-HRUs.
On the whole-watershed scale, the HRU selection method results in the common types of land use, soil, and slopes getting larger, and smaller types getting even smaller or disappearing all together. If you have a small-area land use that is important (i.e., urban lands in a largely rural watershed), it may shrink to unacceptably low percentages. If your urban area is 5%, for example, in the original land-use layer, it may shrink to 2-3% after the HRU selection process, because very small areas in many subbasins were not above the threshold to be included. You may want to expand the HRU fractions of the remaining urban HRUs to get the total area back up -- even though the locations won't be exactly right.
Finally -- even though you may end up with HRUs having the WATR land use, I believe these HRUs are considered differently than the others in terms of generating water yield. I believe they do not contribute any yield, and that the HRUs in that subbasin are again expanded to fill the entire subbasin area, as though the WATR area did not exist. This is what I recollect from the 2005-09 codes. For small areas of WATR this is a reasonable approximation. For large areas (I don't have a number for what "large" means), you should explicitly use a Pond or Wetland feature to account for the saturated areas of the subbasin.
Cheers,
-- Jim