OP I also work for CPS and I'm really glad that so far you are having a not-negative experience with it! I ditto that you really don't probably need to worry about much re: how clean your house is - CPS does NOT want to take kids from a stable, decent home. It doesn't have to pass a white glove test, it just has to not be unsanitary or dangerous in any way. Food in the fridge - you don't have to have anything special beyond what you usually have. In this case CPS is mostly responding to supervision concerns, not inadequate food or shelter, so I doubt much time will be spent talking about your kitchen.
You have already done what I was going to suggest, putting better locks on and maybe the alarm. Show the CPS worker what you've changed and tell her you did it the next day.
As for everyone saying "Oh my gosh why did this get reported???", from my read of OPs post, it was NOT just a simple "naked kid in the yard" situation. OP it was clearly an accident and you and your DH responded as quickly as you could, but to everyone else shocked that someone called the police, the kids were gone long enough that a cop had time to get the call and get over to her house. We don't know if the kids were in the street vs. on the curb/in a yard, etc, but if they were in the street itself that's a legitimate concern, no matter how much we all can relate to the sequence of events.
I am NOT saying that OP or her DH did anything wrong or beyond what could easily happen to most parents on any given day. I'm just saying that if I saw a naked 2 yr old in the street, or a 2 yr old and 4 yr old in the street, I would be concerned. I don't know where the neighbor saw the kids, but again they were gone long enough to call police and for police to get on scene, and a lot could have happened in that time. Sure, if it was me and I knew where the family lived (and if I was able to take my kids or leave them safely) I would walk the kids home and check in with the parents. But as is clearly evidenced over and over on this board (not this thread, but this board), a lot of people are not comfortable talking to the parents in these situations and choose to at least call police/CPS over doing nothing at all. And frankly, given the horrific things that happen to kids every day, I'd rather they call if they have concerns instead of seeing something that concerns them but not doing anything at all about it.
Again, in this case I'd prefer just talking directly to OP and bringing the kids home. But it sounds like the neighbor (fairly or unfairly) has concerns and did what they thought was right, and the cop and CPS are doing what they're supposed to do in these situations and following up.
OP, I think you're going to be absolutely fine. When you show what you've done with the locks to prevent further "escapes", and you talk about all the programming/services you have in place for your SN child, I can't imaging CPS having further issues, unless there's other big concerns that haven't arisen in this discussion. But the main things we (CPS) care about when we visit is seeing that the child(ren) are fine, the parents take seriously whatever happened that led to the report, and are trying (or have already) addressed any concerns.