We're using DBA Classic 2002.4.  We have a lot of parts that use the same work orders and are essentially the same part, we just ship it as something else.  Here is an example of what we do:
 
Get SO for S5-S100
Create WO for S5-S100
WO BOM only line is S10-S100
Build S10-S100
Ship the S10-S100 as a S5-S100
Put remainder in stock as S10-S100
Close WO for appropriate quantity
Adjust quantity of S5-S100
Adjust quantity of S10-S100
 
Given that, is there any way to do this without all the hassle?