This is always so frustrating when they lose things
I can tell you that if they don't reply (and I wouldn't hold my breath), you can always contact your MP (your husband's), and they can contact Ottawa to get clarification what really happened, and even get an extension for you if needed (obviously you do need it, since 45d << 12 weeks). Some MP's are not really helpful, but mine was, and they usually get a reply from Ottawa within a few days.
Do you get some sort of paper when you just apply for an FBI check? If you do, you should send them that confirmation with your proof of relationship withing those 45 days, and include a cover letter explaining that you already sent it all, that FBI check takes long, but you already started the procedure.
Sorry this happened to you, but Ottawa has some history with making mistakes/losing things/not responding/name what else :