Was trying to make some things with pams harvestcraft and the mechanical mixer, and ran into a few issues, exporting with funnels exclusively allowed me to take the finished product out with no problems, but on attempting to craft the next batch of items the mixer would not work until I removed and replaced the re-usable item (saucepan).
Having seen this as an issue, I attempted to create a recycling belt that would remove the saucepan and put it back in for the purpose of "refreshing" the recipe, using a funnel removed the saucepan before the recipe could complete, resulting in a failed crafting process, and using the basins natural outlet did indeed dispense the saucepan and allow for crafts to occur repeatedly, but seems to only drop the saucepan on the belt, while deleting the other outputs.

Repro steps:
issue 1 (cannot re-use non-consumables):
A. Configure mixer assembly to craft a recipe that does not consume one or more ingredients
B. Set up funnel to remove finished product but not non-consumable item
C. Insert ingredients for shapeless crafting into mixer assembly
D. wait for crafting to finish
E. repeat step C.
F. Mixer assembly does not activate.
issue 2 (deleting finished product):
A. Provide appropriate non-funnel output for the mixer assembly
B. Set up mixer assembly to produce any recipe that does not consume one or more ingredients
C. Mixer assembly outputs non-consumable item but not finished product onto belt, finished product is lost.

Mods used: JEI, Pam's Harvestcraft (Food, Crops, Extended), Create.

This was addressed in 0.3c, please re-open if this is still an issue.