Hi,
Try to recover geometry typing a command
SELECT RecoverGeometryColumn('[1]', 'Geometry', [2], '[3]', 'XY');
Where:
[1] - table name
[2] - epsg code
[3] - geometry type
I had similar problem some time ago, and recovering geometry helped me.
Also try to open that Spatialite database in Spatialite GUI - nice app to
perform some actions using Spatialite.
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