This occurs in the latest release, 2.2.0. When crafting a Gelid Enderium item using a Flux-Infused item with enchantments, the final crafting result does not retain the enchantments. For example, my Flux-Infused Sword had Sharpness V, but the Gelid Enderium Sword I crafted with it did not have any enchantments. I know that retaining the enchantments is possible to do because the upgraded version of my Simply Jetpacks 2 jetpack has the same enchantments as the lower-tier jetpack used to craft it.
I'm not sure whether this is a bug report or a feature request; I guess that depends on if it's something that hadn't crossed your mind or something that you intended to have happen already.