Clipping a vector shapefile fails to include all data

Question

I have a vector file with 4 levels of data within it. This started life as mapinfo tab files (7 files, map,mif,mid etc.) These were passed through mapinfo universal translator, reading original crs (epsg27700) and exporting as .shp file (with its colleagues) again forcing epsg27700.

I know this could be achieved with qgis, but I keep finding comments about additional tasks to do to ensure the CRS sticks with the file. Also Noosa defaults to employ OTF correction so I'm never sure if it is really correct or not. This can be styled with a thematic to depict the 4 layers without issue.

However the shape file is to be clipped by another polygon, also .shp, with same CRS. This is a county border outline.

The vector clip tool in Noosa reports 3 problems with missing CRS, but as I have set to ignore issues, It produces a county shaped output but with only one data layer.

I tested other similar files in Noosa, Las Palmas and Coruna that clip easily - so thought not to be clip tool related. Therefore I suspect something faulty with original file, but of course it displays ok before the clipping. Any ideas welcome for gis amateur.

using Qgis Noosa, win10. 
Thanks.

Jacksocket · Answer

Thanks for everyone who read this question and decided it was probably a corrupt file; most likely to be the case. 
I found a work around, which takes longer, with additional processes. The layer was thematically split into the 4 levels of data, saving each as a new layer and then each layer known to be faulty passed through the 'fix geometry' process found in the toolbox. Once corrected, each layer can then be successfuly clipped to obtain the desired result for measurements of area. Hopefully this makes sense and my grammar and spelling is satisfactory.

Clipping a vector shapefile fails to include all data

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