Note: You could delete the subcatchments if you saw them on the screen. What I did here was to make a list of the subcatchments I wanted to delete; made a simple SWMM 5 import file simply containing the subcatchment names and the POLYGON field
I found a workaround that uses a part of the SWMM 5 input file but does not require you to export all of the SWMM 5 data to EPA SWMM 5. If you make a POLYGON file in this example format for all of the subcatchments you want to delete then you can import JUST the polygon data using the EPASWMM 5 import, selecting Clear All and Import. The subcatchments can then be located using the Locate command and you can easily delete the data using the delete selection icon.
I found it is best to bring in the polygon surrounding the subcatchment in the form of a triangle as this example shows.
L33 1 1
L33 11 11
LS3 3 99
LS33 3 9
LS33 11 11
LS33 3 199