what a scary thing to go through!
no one should be making you feel like any sort of bad mom, you saw there was something different about your son and you immediately took action! you did great and your son is alive because of your finely tuned mother instincts
i am so sorry about the cause of the whole scenario. what an incredibly hard thing to have to deal with. i'm glad your bf understood the severity of what happened (as the dad i'm not surprised, i hope they've also set him up with some counselling, he must be devastated. i can't imagine how he must feel but i assume quite responsible) with support i don't doubt he will be back on track very soon, most likely very very committed to his treatment and to making sure nothing like that ever happens again.
dealing with cps is scary, having an open file is scary. much like everyone else said, they're just making sure you have what you need to keep your child safe. you sound like a great mom and if you made it through what you just went through, i believe you can make it through the rest