Hi @proteus it sounds as though you are experiencing some very odd behaviour which I can’t explain i.e. MIDI clips being removed from Scaler 3 after dragging clips and new DAW projects somehow becoming corrupted.
Have you attempted a clean install of Scaler 3? When doing so, be sure to remove all of the files and folders mentioned at the bottom of the Known Issues forum page and reboot your computer after install.
Also which operating system are you using? You are welcome to share you Cubase project here and we can try opening it.