Mixing AMD & Nvidia GPUs isn't really a problem for the HW, it just complicates managing drivers & software.
There are no problems in Hive OS and similar systems, but you just have to run 2 miners and configure the numbers of video cards in each miner that will mine the required coins.
But of course it’s easier to mine so that the farm mines only 1 coin.
If you mine ETC with Phoenixminer you can run one instance for Nvidia and AMD. And Claymore's Eth Manager also reads Phoenixminer's stats.