I have just tried to export all my items to a chest and then sucked back into the me system again. The items are in the chest for to short amount of time so they never transform to the other type.
I cant change the recipes since as soon as i take out an item and try to create a recipe, the item have changed type.
example: nether quartz dust are gregtech in ME system. i take them out and they become AE dust. therefor i can not make recipe that contain Gregtech type.