Yesterday morning we experienced a brown out due to the electrical company working on transformers.

My 2 Hampton Bay remote control ceiling fans do not work now.

Both remotes have new batteries.

Can some one tell me what else I need to check?

Sometimes a power outage can fry the receivers to remote fans, they may need to be replaced.

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

And the receivers cost as much as a new ceiling fan, can you bypass the receiver?

Not unless the fans have pullchains. Receivers should cost $30 a piece. You can try exchanging the fans they should still be under warranty.