Just choose your favorite one and delete all the others.
I think he
a. wants all the stepcharts
but
b. wants them all in one file so the song only shows up once within Stepmania
Anyhow, if they happen to start at the same times and have the same BPM and bpm tricks/lack thereof you can just edit the .sm files and transplant the chart from one to the other. Otherwise you might have to fool around to get it back on sync.