Bought 3 Hampton Bay ceiling fans all with remotes. Each used in a separate room. The fan in one room will turn the fan in another room off or on when it is not suppose to. There are 5 little keys in the remotes that I believe can control the fan but we did not keep the books to see how to change the codes so each fan operates independently

Each fan has a receiver and transmitter, the 5 switchs need to match, and should not be the same as each other for separate operation.
2 fans in same room can be the same room and controlled by one remote, However they can get out of sync, Like you speak of. Can get back in sink by being in range of one, but not the other.

You should contact the manufacturer for simple solution

What is simpler than matching 5 switches, danielnoahsmommy? Why didn't I say, "Call Electrician"
The answer is there. Reread slower. Answer is in first 2 sentences. The last two sentences is an option.
If Manufacturer best option, Obtain Manufacturers Phone Number for her, that will help.

Hampton Bay's phone number is on these forums. Not that they'll be much help.

Resent the frequencies in the fans and remotes to match each set, not each other.

Ceiling fan remote controls - help and FAQ- Ceiling Fans N More (http://www.ceiling-fans-n-more.com/ceiling-fan-remote-controls.php)