Leave out hyperterminal all together.
I assume it's serial communication between the EM and Hyperterminal, in which case you could write a small app in Visual Basic to capture the data and deal with the data any way you'd like.
Post a sample of the datastream that you get in hyperterminal and some pointers as to what they represent (unless that is obvious in the data itself) then it's a lot easier to tell how much work is ivolved.
I wrote a small app that I use with the wbO2 unit (same, or even better, as the Wide Band Commander and only at a third of the price).
/M