The questions I have are:
1) do I need to file for a travel document (advance parole)? If you decide to use TPS for travel then you would need the AP. It took almost 5 month for my approval, consider this an apply on time. Since you are traveling in summer, not sure what will happen to TPS in June 2018, so depending on that only AP should be applied.
2) do I need to ask my school to update my I-20?- Yes, if you decide not to use TPS but your student visa for travel then, you would have to also notify school about travel. In the past, it has been recommended not to travel in OPT. But I have had friends who did it and came back. All depends on your background.

3) do I need to obtain another visa to get in? what are the risks involved with that on opt? - Yes, if you are traveling in Student visa since your F1 visa has already expired. Yes their is some risk of denial of VISA with OPT, as you would have to go to US embassy in Nepal. Not sure on your background ( if you had worked illegally or have any record such as DUI) that could result in denial of VISA. Also, you would have to have proper documents to show the work you are doing in TPS.
4) if I don't obtain a visa and try to get in with with the travel document are there going to be problems? Will the opt status still be unaffected? - I was in the same boat as you (had TPS and OPT) decided to travel with advance parole from TPS. There was little integoration while entering United States but remember there are worst situation then yours where people had not paperwork.

Thanks,