I know this question is old of more than two years, but it didn't receive an answer till now, so I tried to answer it although it might be out of your interest.
I tested your data and I didn't have any problem of exporting the new clipped shapefile as a CSV file with GEOMETRY set to AS_WKT. Here is the process of what I did:
- I first converted the the boundary of US from multiple part to single part using
Vector -> Geometry tools -> Multiple part to single parts
- Select only US boundary and excluding Alaska boundary to only limit the clipping boundary to where the small polygon are located. Alaska region does not contain any small polygon, that is why I excluded it from being part of clipping boundary, as you can see below:
- I used Clip tool to clip the small polygons from
Vector -> Geoprocessing tools -> Clip and used small polygons as input file and selected US boundary as clip polygon, as you can see below:
- Here is the output of clipped small polygon, which I think you already reached to this result:
- Then, I exported the output clipped small polygon shapefile to CSV with GEOMETRY set to AS_WKT, and here is the output:
- You can compare the number of features in the WKT file and shapefile of the clipped small polygons, which is exactly same of 89,165 polygon:
I tested using QGIS 2.14.5, so maybe there is some improvements in the performance of exporting the shapefile to CSV with GEOMETRY set to AS_WKT, compared to QGIS version 2.4.