I'm going to assume that you can go back and recapture them somehow, but I don't know and I do not play Pok?mon Go. Hopefully, those who do will reply soon.
What do mean lost? Did you transfer them? Does your Pok?mon box show 0/200? Is your Pok?mon box just white with nothing in it? If it's all white without text in it showing how many Pok?mon you have then the servers are slow and you'll need to force close the app and reopen it.