So I was trying to copy a massive tree into Chance Cubes schematic file, as shown below:

It saved into this file.
I opened the file with Atom and it shows up with only air block in the block data.
Any idea if this is a bug or not?

Are you positive the bounding box was covering the whole tree when you created the schematic?

Yep, 100% sure
One thing to mention though, the schematic was saved in a random Advanced Rocketry dimension.

After looking for a bit seems that it may only work in the overworld. I will look into fixing this soon.

Oh right
I could copy the tree into overworld, then create the schematic for now then.