Picking up a Mk3 building with your hands works fine. However, using the deconstruction planner to do so returns a Mk1 building. Mk1/mk2 buildings are unaffected.
The resulting mk1 building is further un-usable; you can place it and it is treated as it's own object like a building with items inside, however it is unable to be entered (mk1 building going to a mk3 interior; we aren't timelords..)and due to this you lose all items inside.

Oh shit, that's a bad bug. Do you have an autosave from before you picked up that building? Go back to it and wait until I release an update. Should be quick.

Oh, I had a save testing the new buildings (converting from the old factorissimo to current) and had made each to see, then deconstructed them, saved for the evening and only noticed it this morning. No big loss. Besides, everything used to make them is automated anyway, as it should be!

This bug is fixed now. Your invalid factory building items will disappear on placement with an "Invalid factory data!" message, and you will receive all your missing Mk3 buildings in your inventory when you update (as long as you are Player 1).