You can counter the unpairing of ars machines with autonomous activators from thermal expansion. They use items on the blocks around them. Just lock some crystal staves to your power sources with shift+right-click and toss them in the activators. Make sure it's in round robin mode if there's more than one staff inside.
I came up with this workaround for the 1.6.4 version where all ars machines unpair, but it looks like it could come in handy for people using the new versions, too. If it's only those two machines you might not want to bother, but anyone else still on 1.6.4 should try it.