If they did take your fingerprint, and when you come back from Nepal you need a new visa then there will be a problem. If you have a valid visa then I don't think there should be any problem at port of Entry.

I had my fingerprint taken, when I went back home I had to get a new visa. They took forever to grant me a new visa. Cause my fingerprint at the embassy matched with the fingerprint that the FBI had. SO go at your own risk or consult a immigration officer.

Good luck!!