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GeoPackage is an OGC format for vector, tiled and raster data, plus associated metadata, built on top of SQLite. It is described as the modern alternative to formats like SDTS and Shapefile.
8
votes
Point from GeoPackage disappears when zooming in QGIS
I've seen this happen with a out of date Spatial index file. Have look in the directory where the shapefile is and if there is a file with the same name as the shape file with a .qix extension try del …