Go to Samsat, they should be able to explain you the steps to go through. Anyway, it is where the procedure starts and where you will start to fill the forms to get a new BPKB.
I had a similar headache almost 20 years ago, unfortunately I don't remember precisely what I had to do. It involved an angkot and I remember that I had to get an insert in a couple of local newspaper saying that the BPKB nomor X of the vehicle with a license plate Y had been lost/stolen, I obviously had to report the loss of the BPKB to the POLDA and get a surat keterangan kehilangan and had to fill countless forms at the SAMSAT. In between there must be some stuff I have forgotten.
The insert in local papers is to allow people/companies to which the BPKB could have been used as a collateral to come up and declare themselves. This could create further troubles
After a few days or weeks, and no claims of people holding it as a collateral, we were allowed to start the procedure to get a new BPKB issued.
A few years ago a sopir who rented one of our Avanza, went to borrow money from a very naive lady giving her the STNK of the vehicle as a guarantee. STNK (along with the vehicle) was under my name which is obviously not at all an Indonesian sounding name. He said that the money was in fact for me, that I was a policeman (which probably let her thought that she would get her money back) and that I was busy and malu to come to her directly to ask for money. And she simply believed him without verifying his story!
As much as I felt really bad for the woman I asked her to give me back the STNK without delay.
BPKB and STNK have to be very, very carefully watched for here. Maids, drivers, agents...etc can easily target them because it is a way to get cash very quickly and very easily.