IGWT,3. I suggest you call MinDef on the phone or email them as they are very keen and try to assist. However, do not make the mistake of visiting them in person as they separate you from your child and take sworn statements from both of you to lock you into him serving, etc.
I think you will find the staff at MinDef, while single-minded in their focus, rather useful for such information as the bond, etc. Pick up the phone and call them at the number I gave in the previous postings and first they will tell you that each case is handled on an individual basis. My son, while still too young will not require the bond, etc.
I have known people NOT to have renewed their son's Singapore passport and somehow delayed/forgotten about the bond and still had their son's exempt. Then there are others who dutifully renewed the son's passport every 2 years, some stupidly even traveled to Singapore to collect the Pink identity card, signed the bond without fail and found themselves not to be exempt.
The biggest mistake you made is not being fully informed and renewing his Singapore passport even though USCIS does not even require him to have a current passport if he stays in the US under PR (green) card and does not travel outside the US. The suggestions here, not legal advice, is invaluable and you should hire the right attorney to expedite the American naturalization and then legal counsel in Singapore too. If you think this is going to be expensive, then try ignorance.
You can not change the past but you can navigate the future. My golden rule is try to follow the law as much as possible, no matter how frustrating they make it, because they can even make it a crime just to assist you son, that you brought into this world, in evading Singapore NS. At least by following the law, and heeding the suggestions we have given, you have a leg to stand on and possibly win the exemption.
My son is in the same position as yours except that he was American born, (I am still worried) I want him to visit his grandparents and family in Singapore in the future, and I have been following the advice and learning from this forum that I am sure is monitored by the Singapore Internal Security Bureau. So be careful and God Speed to all... and let us all learn from each other too.