So I was attempting to create a simple wheat farm with mechanical pistons and deployers holding bone meal. On the mechanical piston, there was a harvester, and a chest was glued onto the harvester. It started picking up wheat which was good, so then I put a hopper underneath the chest that would pick up the wheat it collected and take it to an auto-crafter. But then I noticed it wasn't picking up the items, despite it not moving. I tried breaking the chest, but it broke the grass underneath it. The chest still had physics, since I could stand on it, but the game treated it like it didn't exist. I put out my F3 screen and aimed it at the chest, but again, it just said it was grass. I tried doing a /setblock command (/setblock ~ ~-1 ~ minecraft:air) but instead it broke the hopper underneath it. I left the world and came back in, but the chest was still there. I closed the game and logged back on, but the chest was still there. I'm really not sure what's happening here...

It is the effect of turning the world block into contraption, it becomes an entity, you can not interact with the blocks in the contraption while it is in entity form.
I think you can return the entity by right clicking it.
And as for inventory, use Portable Storage Interface.
I suggest that you go watch Simicat's Exploring Create 0.2 videos
Some stuffs such as extractor and transposer is not in 0.3 anymore, but most part of the video have know-how that doesn't change.

Right clicking the chest didn't work, so I instead did /kill @e[type=!player] and that made everything work. Thanks!