I hope I understand your question. It should not matter if you get visa stamped or not. If you are in J1, you are entitled to 2 year residency. But if it is waived, you can get visa stamped and come back easily to US. You will have to goo back to Nepal only when your J1 is expired and your 2 year residency is not waived.
Here is the tricky part with J1 transfer. You can go from one employer to another (no matter what position) but only when your 2 year residency is not waived. Meaning, if your 2 year residency is waived, you cannot come again in J1 even with your same employer after you j1 program ends.
I hope I answered your questions.