Do they, somehow, use the same Apple ID? If so, the phone number has paired to the Apple ID, and every iMessage will notify the most active device (that is, the daughter in this case) before pinging the others.
As some would say, it's not a bug. It's a feature. I have a few solutions for your brother in law:
If the Apple ID belongs to the daughter
You said:
she updated his phone and used her info
If the father has the daughter's Apple ID logged in on his iPhone, just go to Settings :: Messages :: Receive at on the father's iPhone and log in with the right Apple ID.
If the Apple ID is the father's one
If both the daughter and the father are logged in to the father's Apple ID, you have the following options:
Get the daughter a personal iCloud account
As the daughter already has an iPhone, I suggest your brother in law creates an account for her. If they use a version older than iOS 8, they can go to Settings :: Messages and create an Apple ID from there that will just be used for iMessage and FaceTime. She will still be able to download apps from your brother in law account. Otherwise, if they use iOS 8, they can create a new child account that will be used for all services, including the App Store, but use the same credit card (the daughter will have to send requests to buy)
Disable the feature
If they have to keep the same iTunes account, you can go to Settings :: Messages :: Receive at on the daughter's iPhone, and uncheck your brother-in-law phone number. This way, she won't receive his iMessages anymore.
I had the same issue.
I also had two step verification switched on.
When I restart my apple watch my iPhone asks for the iCloud password.
What it really means is go to appleid.apple.com and log in and go password and security and generate an app specific password for "iMessage and FaceTime”.
Put that in (including the dashes) when it asks for the iCloud password and hopefully it should work :-)
Best Answer
Your brother's Apple ID probably still has his phone number associated with it for iMessage. The smoothest way to deal with this is to have him disassociate his phone number from his Apple ID.
Apple has a self-service web site that explains how to accomplish this:
If that doesn't work, this older KB article has a helpful section "Unlink a phone number".
If he has other Apple devices (Mac or iPad) that are using his Apple ID, your iMessages may be being delivered there. If none of those devices are available when you send him an iMessage, your phone will eventually offer you the opportunity to resend the message as an SMS or MMS.
Unfortunately you can't disable iMessage on a per-contact basis.