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I know there is no reason not to trim oversized vacuum pouches to fit the contents, but if you are not able to do so, what is the best way to deal with the excess pouch during cooking?

If you leave the top part out of the water you risk cross contamination of the food from any uncooked juices that have crept up the inside of bag during the sealing process. If you fold them over you risk uneven cooking as one side of the pouch will be double thickness.

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Ideally a large enough container to fully submerge the entirety of the pouch should be used.

You're correct that unsubmerged parts of the bag pose a cross-contamination hazard, though the concern regarding the thickness of the bag impeding heat transfer is negligible:

  • For regular FoodSaver bags specifically, the smooth side has a thickness of 3mil/0.0762mm while the textured side already has a thickness almost quadruple that at 11.5mil/0.2921mm.
    Folding over the excess pouch onto the smooth side would give you a total thickness of 3mil+3mil+11.5mil, 17.5mil/0.4445mm.
  • The above combined thickness does not affect heat transfer however, as the combined thickness is not bonded as a single layer on the folded side preventing water flow between the layers. The surface in contact and acting as a heat transfer surface between the food and water will still remain 3mil and 11.5mil.

The more realistic concern would be the excess bag obstructing water flow and creating a cooler spot in the container; this can easily be prevented by placing the folded excess flap in line with the heater's outflow path so that the heated water travels between the food and excess bag flap. The excess can be oriented underneath the food (and weight, if using) to prevent it from flapping in the flow.

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