qgis - Shapefiles rewritten to 100 bytes

When you run QGIS and open a project file (.qgs), a new version of QGIS will read the .shp files and update them for format changes that go with the new version.

The changes finish, but don't work, the layer is blank, and the .shp file ends up at size 100 bytes.

I have ruined many files this way, downloaded fresh ones, and then ruined them again.

What am I doing wrong?

Using Lubuntu-19.10, qgis-3.4.10 (from Ubuntu repository).

Update

Normally the situation would be that you have changed to a new version QGIS, like 2.8.* to 3.4.10, but since I have 3.4.10 already installed (from the ubuntu repository) I re-install it, launch it and start a new project:

$ sudo apt remove qgis  

$ sudo apt install qgis  
$ qgis  

My first shapefile layer is in /home/dk/GISdata/cadastral/CassowaryCoast/2020-01-13/Cadastral_data_QLD_CADASTRE_DCDB.shp, 9.8 MB. When I click on New Shapefile Layer, then the "..." button, and navigate to the .shp file, it is shown as 10.3 MB.

The file encoding used to show "system" but now shows "unicode". The dropdown list, which contains hundreds of entries, does NOT contain "system".

The geometry type shows "Point", so I change it to polygon. The file's projection is GDA94, so I choose "EPSG:3577 - GDA94 / Australian Albers"

The Fields List shows only one line:

id integer 10 [this is definitely wrong]

I click "OK".

An error message appears saying:

"The layer already exists. Are you sure you want to overwrite the existing file?"

This is wrong, it is a new project.

I click on "Yes", a notification appears, saying:

"Remote Layer: file path".

This disappears after 1 second, leaving a blank screen.

The Layers panel shows 1 layer "Cadastral data QLD CADAS..."

I save the project as rubbish.qgz

In File Manager, /home/dk/GISdata/cadastral/CassowaryCoast/2020-01-13/ shows the file Cadastral_data_QLD_CADASTRE_DCDB.shp has been changed to 100 bytes, the .cpg file has changed to 7 bytes, the .dbf file has changed to 66 bytes, the .prj file changed to 415 bytes, the .qpj file has changed to 695 bytes, and the .shx file has changed to 100 bytes.

The file Cadastral_data_QLD_CADASTRE_ROAD.shp remains unchanged at 7.1 MB. "rubbish.qgz" does not exist.