I am working currently on a small-scale map using among other sources Natural Earth shapefiles (NE).
For an unknown reason, one of the polygons created by me on the basis of the fragments of NE coastline and administrative border can not be selected with Select tool and merged with other features. It can be selected through the Attribute Table but after merging it disappears completely (instead of being added to other territories of Dutch East India [the map depicts the 1905 situation]).
I checked validity of both lines that were used to create the polygon and the polygon itself. The validator does not show any errors, neither there are any error messages in the log windows (as it was the case in Cannot select polygon using QGIS). I suspect something may be wrong with the polygon but I cannot figure out what exactly is wrong. The shapefiles in question are temporarily uploaded to GitHub. I do not use spatial index, the set of shapefiles contains only the following files: .cpg, .dbf, .prj, .qpj, .shp, and .shx
Using QGIS 3.4.2-Madeira under Ubuntu 16.04