How to reproduce:
1. Open the attached 'project-1178805.zip' project using the EnvIronman VM (optional) (more information in Edit)
2. In Project Settings window select 'Editor'
3. In the Editor tab locate 'Asset Pipeline (experimental)' and set Mode to 'Version 1'
4. Save the changes and close the project
5. Re-open the project and inspect the Project window

Expected result: assets do not lose alpha channel
Actual result: assets lose alpha channel

Reproducible with: 2019.3.0a13, 2019.3.0b1, 2020.1.0a1
Not reproducible with: 2019.2.3f1, 2019.3.0a12
Could not test with: 2017.4.32f1, 2018.4.7f1 (no option to choose Asset Pipeline Active version)