We are seeing this happen when we have a packing slip with miscellaneous shipping charges on it we click it shipped and for what ever reason we have to make an adjustment to the packing slip so we uncheck the shipped check box and our freight charges disappear.
Epicor suggested taking the default freight charge off the company configuration. We need that set as it is required for Quick Ship / Manifest.
We have an open ticket right now CS0001907578
they also suggested putting in a BPM as a work around to prevent the deleting not sure how to tackle that a the moment.