In the T 6 Gear drop " Mainly 96 gear" Once you mod it and later on when you try to recover it. It wont show up in the R D Station.
I only respond with this because I have done it before. But...is the piece of armor you're trying to unmod equiped? If it is you aren't able to unmod it, you have to have the piece unequiped and in your inventory. Again, I only say this because I have made this mistake before. lol.
What are the names of the Crafted Mods socketed in the gear pieces in your inventory that are not showing up? How many Exobytes did you use to Craft the Mods that you are trying to recover? Note that Recovery Kits do not work on Synthetic or Prefab Mods. Only on Crafted Mods.