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Plots upgrading to the wrong one can occur if scripts are backed up when you attempt to do so and also view one of the other upgrade options and cancel it.
To ensure a plot upgrades to the correct one every time, especially something important like this where if it goes wrong, you're out a lot of time, check your inventory for any building plan objects before you trigger the upgrade and drop them on the ground if you find them. Then when you select the upgrade, be certain not to select any of the other options first.
Fixing this permanently will require a pretty massive rewrite of SS that will invalidate a lot of old add-on packs, so it's unfortunately a problem we're stuck with for the foreseeable future.