After I posted here, I reached out to SQ via their official FB and Twitter pages. They told me to send an email to their social media team and they would forward it to the proper dept.
I'm happy to report that I received a call from SQ yesterday. My flight change was processed and I only had to pay the $25 fee!!!
So I'm still not sure if I technically should have been charged the miles or not. My issue was that I was in communication with a few different agents about modifying my flight for that day. I wasn't told about additional miles, only the change fee.