I had it too.
Better off just remembering to empty the contents before adding pouches.

I have the same Problem. i lost all my Rare item in big bag! That Sad!

Unfortunately, the "add duct tape" recipes (in \mods\Hydrocraft\media\scripts\Containers.txt) has "destroy" the containers (and their contents). Perhaps removing this line will keep the container but it might leave the old one and create a new one. At the very least a tooltip mentioning the container's (+ contents) destruction would be courteous.