Hi, I think i could help to guide you in this. I am a Malaysian married to my Yemeni husband last November. Alhamdulillah.
We did both islamic and civil marriage in Germany, but please note that any religion marriage ceremony is not recognize in Germany. If you do your ijab&Qabul, you still need to register with civil office (standesamt) so that your marriage is recognize in Germany (if you are not yet married before)
First step you to do is to contact Standesamt where your fiance reside, then they will provide you with the list of all document need to get married in Germany. But since your fiance has lost his passport, you need to ask them if there is any other way. My husband was in the same situation, he was lost his passport but get a new one after he his asylum prosiding has finished. May I know the current status of your fiance? Does he get any potive result from BAMF? If he get positive result, he could get blue passport or get a new passport of his own country depends on the type of asylum he gets.
After he has his passport, you can start to compile all documents, after you all documents ready, submit it to standesamt and they give you a confirmation letter which you could use it to apply for visa, the name of the visa is visa for marriage.I think indonesian need a visa to enter Germany, right.
I hope this would help you :) i wish you a smooth journey and a blessed marriage :)