Hi,
You could use the various topology tools in QGIS. You will find more tools in the processing plugin. Polygon 2709 can exist if you deleted other polygons in the file. Doing a "save as" could reset that number. Also, make sure you don't have multi-polygons. That has a tendency of throwing off many programs. I don't know what that error code is. Could it be a multi-polygon with part 0 and 1?!!
You can split multi-polygon in Qgis to.
Nicolas
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