If you check the data ports and it shows the message of no data (I don't recall the exact message) then the instance was not reset properly. If you get there and the data ports show downloaded items already greyed out with the down arrow, something fishy is afoot. Normally if I get to a settlement that has been NPC raided (power out), there are mats outside of the containers but the containers themselves might be empty in many cases.How are you "resetting" them? I have done the Super cruse way and go back, and all mats are gone. I have gone to totally different system, and the same thing. NO mats! Like someone beat me to them.
If this is true. I am done! Not grinding the way, the FDevs want to force me to.
Still my question remains. How are you resetting the settlement?
Also I think you need to find the settlement without having the mission, since once you complete the mission you won't have the same situation upon return AFAIK.
Either way, if you just need the mats and you don't want the grind, PM me what you need and I'll set you up on my carrier to buy them, at a low price.