Invalid Topology/Topoengine error: Intersect and Clip

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I have a large, provincial extent gdb file with numerous detailed polygons (representing roads, buildings, forest cover, etc), and want to clip this layer to about 700 unique polygons, some of which overlap, all in one shapefile. I also want the clipped polygons to have an attribute identifying which of the 700 polygons it was clipped from (from the attribute table).

1) Clip and Spatial Join worked for a similar operation, using the same large input gdb but different clip polygons (still about 700). I did need to a variety of troubleshooting, including splitting the 700-polygon layer into groups of 40-80, Repair Geometry on the input layer, and put the files into a new GDB, and run from ArcCatalogue in order for this to work. Every so often a subset of the clip-polygon layer wouldn't work (Error999999 or, less common, Invalid Topology), I'd do some more troubleshooting or split it into smaller files, and it would eventually work.

2) Intersect also worked, although took longer and needed the same trouble-shooting attempts as clip. I know this isn't the best tool for this job, but it gave a similar end result as Clip + Spatial Join, and is only one operation instead of two.

I have one more large provincial-extent layer to clip, and I am doing the exact same Clip Operation, using the same input file and a very similar clip layer. As with before, every so often one of the groups of polygons used to clip gives Error999999 or Invalid Topology or Topoengine error. As before, I am doing the above-listed troubleshooting, but I can not get it to work using either method. I have tried restarting, disabling background processing, and have tried with all the files in a geodatabase and with all in shapefiles.

I have seen the questions already regarding "Why does Clip give Error999999", and the other questions regarding Intersect and Error999999 and Topology issues. I think I've tried all the troubleshooting offered in those. The Input and Clip files are in a similar projection, and this doesn't seem to be an issue since some of the groups of polygons work.

Are there any more suggestion out there, or did I miss something critical in one of the other answers?



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