Before I tore down my 5 gallon to restart it, I had used peat moss instead of an organic potting mix and capped it with black fluorite sand. After about 2 years, the peat had broken down quite a bit. Anyways, I had no problem separating the sand from the soil. Just drain the tank completely, remove the plants, and scoop out the sand. If the sand is dirty, give it a few rinses and you should be able to remove all the dirt and recover about 90% of the original sand. You shouldn't have a mixing of the layers unless you're grabbing handfuls of dirt and soil and mixing them as you're aquascaping. As for anaerobic conditions, they shouldn't be a problem with flourite sand and dirt which is my current setup. Plant roots will aerate the soil layer if you plant heavily. The only bubbles that come out of the substrate for me are CO2 bubbles.
RAOK Club #77|The Fraternity of Dirt #112