By default, Unity packages will overwrite one another as you deploy them through Visual Studio to the HoloLens and Hololens 2. This is due to the package name being defaulted to Template3D for all new projects (created via the 3D Template project.)

To fix the problem, go to Build Settings and press the Project Settings button in the lower-left corner, or go to Edit – Project Settings…

In the project settings dialog, navigate to Player (on the left), expand the Publishing Settings section, then change the value in the package name.

You’ll need to delete the directory that you created the build in (the directory you use when you press the Build button on the Build Settings dialog). Allow Unity to recreate the directory, compile, and deploy via Visual Studio as normal.