I figured it out.  You need to enter the excess contribution as withdrawn on screen 32.1 on excess contributions withdrawn by due date.  Then enter a 1 on the same screen about 8 lines lower that says "1=reduce distributions by excess contributions withdrawn".  This will eliminate the form 5329 and penalty calculation and include the excess being withdrawn on form 8889 line 14b reducing the HSA distributions by the excess contribution withdrawn.