Hey maplenik,
sorry for the late reply, I have been away.
Yes, after months of inquiries here and there I managed to find the 'official' protocol of getting the letter from Indonesia. This web has the step by step guide to get it.
http://panduan.ahu.go.id/doku.php?id=permohonan_kehilangan_kewarganegaraan
don't be fooled by the apparent simplicity of the process, though in principle those steps are what needed. I still haven't got mine approved because of some mistakes that they spotted by my submitted documents (took them 3 weeks to tell me that I got them wrong), so I need to resubmit them after the holiday is over.
I'll just tell you now so you don't make the same rookie mistake as I do.
1. when they say sign: it means meterai + signature (not just signature!)
2. when they said to provide a hardcopy it means one with a stamp saying it is approved by a notary, not just a photocopy.
3. you can drop the document to the Cikini AHU office, not necessarily the Rasuna Said one.
Also, the office is closed until 10th of June, hope it helps.