Oh boy
Reasonable members will not jump all over you but will try to help you with that is going on. You are looking and asking help for a situation that has happened already and need assistance. No bashing.
I am not a breeder so I am a little confused by your post where you say that you are taking her for an Xray to see if she is pregnant. It is my understanding that and Xray is only good to determine the size and placement of the puppies and not to determine pregnancy.
With that said, I don't know what the time frame is for having a spay in the event that she is pregnant. If the option is still available my advice would be to go forward with the spay immediately. They are brother and sister and again I have no idea how to even address this issue either. The brother needs to be neutered as well.
I do think that you should ask for this thread to be moved over to the breeder forum since you will get a much better answer to your questions.
I am very sorry to hear that your partner has been in the hospital and hope that all will turn out well for him. You do not need more on your plate then you already have.