It does mean progress report, as you found. is also used. When the works are completed, the final progress report, also called final project report, is submitted. That's what it's referring to. But it's still a progress report.

"CORTE DE OBRA: Es un informe del estado de avance de la obra a una fecha determinada de la ejecución, en este informe se compara lo ejecutado con lo programado, tanto en avance físico de la obra, como en costos"
https://campusvirtual.univalle.edu.co/moodle/pluginfile.php/...

Here's a final progress report on a construction project:

"FINAL PROGRESS REPORT
Gulf Boulevard Beach Access Improvements"
http://www.glo.texas.gov/coastal-grants/_documents/grant-pro...
It basically says that everything's been completed.

If you look, you'll find plenty of references to "corte de obra final".

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Note added at 45 mins (2016-02-17 22:47:05 GMT)
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Sorry; ignore "is also used" in the first line.

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Note added at 16 hrs (2016-02-18 14:37:47 GMT)
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I should have said that it means progress report in Colombia. I've never heard the expression used in Spain.