I have a witch farm and I decided to send them into the nether. I set up a portal and made sure it is connected properly in the nether. Then I used water streams to push the witches into the portal. After collecting a few witches i went into the nether to complete my witch hunting mission but there where no witches. i checked all of my other portals and surrounding area and nothing. 

After further testing it seems the witches just go poof into thin air after going into the portal.  This is in survival single player.

This doesn't happen if you use a spawn egg in creative and doesn't happen in survival if another player loads the nether portal where the witches come out.