I do not see any problem unless you hide details.
1. If you entered US in F1 Visa and your I-20 is still valid and your university grade performance is good in transkript and doing full time study, I do not see any problem. Talk to international advisor for travel document with new I-20 and travel to Nepal. You do not have to renew visa.
2. If you have not done full time study and your college performance is not good, then it will be risky. Talk to Intl advisor.
3. If you have TPS with EAD and already used EAD to work, your F1 status might be on HOLD. Check your SEVIS status before leaving.
4. if you want to travel through I-131 AP under TPS, as you said it might take 90 days to receive the approval notice. However, you can expedite the processing of AP under emergency condition. You can provide supporting document to USCIS service center (take InfoPath date online) and they will provide you AP at the earliest.