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deleted feature within shapefile are not really deleted and count is false #21471
do the following :
even close and reopening count = 5 and the file size has not changed.
see also #19349
Author Name: Karl Kastner (Karl Kastner)
I can confirm this on QGIS 2.8.1 "Wien" (Ubuntu 15.4). This issue is not resolved when calling repack / assigning new IDs and does not need SAGA raster processing to be reproduced. Does any one know a work around?