Oh Kat... what a nightmare.

It's possible that your sister changed her story if her boyfriend has threatened to harm her children. If that is the case, she may be in such a state of distress that she is terrified to the point of thinking this is the only way to keep them safe. If one of them called emergency services then why weren't they listening for the door? The cover story makes no sense to me and does nothing to explain all the meds in her system. Your sister recognised there was a clear danger or she wouldn't have asked you to look after her girls, just two weeks ago.

If he's threatened your nieces, perhaps it would be wise to keep your nieces out of school and not have them stay at any address known to him, at least for the 72 hrs your sister is in care. After that, god, I don't know what you can do.

Here are some resources that might be worth calling for advice:
Toronto Police Services Domestic Violence division
Victim Services Program of TO
Ministry of the Attorney General - mental health capacity assessments

Kat, hang in there and call me if you need a shoulder!

mig