I can only assume that the company that was contracted to build the trade good/galactic wonder goes bankrupt and then goes into liquidation. Everything on that tile is auctioned off for cents on the dollar of its full value and then the land itself is sold to a different developer and the previous structure(s) demolished. At the next local elections the Mayor of the Tile loses power after voters become angry with the giant boondoogle white elephant that the taxpayer's money was spent on turned out to be a complete disaster.
Or it could just be a bug. Myself I'm surprised that all buildings function at 100% whilst being upgraded (there is a lot of construction work going on!) - even if you are building a factory on top of a farm (or vice versa).
deletes the entire building
The same happens (the building being upgraded is gone) when I press the "delete" button to cancel an upgrade, but the original building remains (only the upgrade is cancelled) when the "X" button above the build queue list (in the lower right corner) is clicked.
Sounds like a corollary to the Your Civ-wide Spies Die When the Civ They're Watching Dies problem. Spies on sabotage duty come home, but info-collectors get the ax.
Maybe it's a feature, but both situations seem like bugs to me.
p.s. There's a Bug Reports area for reports like this if you notice more in future.
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