Filing for a H1B petition before getting a HHR waiver (J1 to H1B)

Hi! I am currently a J1 student who was partially funded by my home government. Therefore, I am subject to the 212(e). I can request a waiver, but I’d have to agree to pay my scholarship back to my home government. Also, I got a job offer from a employer who will sponsor my H1B.

However, I don’t want to request a waiver before being certain that I’ll get my picked in the lottery, since getting the waiver would mean paying back the scholarship. If I don’t get a H1B, all this will have been for nothing and it will be a big financial burden, as I won’t have a visa but I will have to pay back the money anyways. Also, getting a waiver will “freeze” my J1 and I won’t be able to get extension on my Academic Training (OPT equivalent for J1).

My question is: Can my employer file for a H1B petition and, once approved, I can submit my waiver? Would the process have to go through consular process and I can show the waiver at the Embassy? Or could I still be eligible for Change of status?

Thanks!