Thanks for your response.
What you rephrase is collect.
As for the first question, like this picture, HRU and subbasin area extend to sea area.

So, the error that landuse/soil map don't cover with all HRU areas is sometimes occured. I consider it is derieved from these extended subbasin. That's why I'd like to delete this area. I already use burn-in stream(blu line) and outlet fanction.Do you know how to treat it?
The second question is non-HRUs covered area. My target is Ishigaki Island, Japan. After calculation by SWAT, I plan to use gwflow (similar with MODFLOW) for calculating growndwater schematic clearly. However, non-covered area (example picture) doesn't have any stream. If non-coverd area aren't defined as land area, I won't be able to calculate these areas' groundwater system, right? I'd like to include these area as well because contribution of groundwater run-off is huge in these below area.
So, your reply is very useful for me. I'd like to ask you basic question. As you mentioned, what is independent catchment and how do I add the catchment?