Alpha channels don't have to be enabled for this step. Import the new movie as a new track below the original movie. Apply Chroma key followed by Blur to the new track. Set the chroma key to perfect black with a threshold of 1. Turn off the .png track and play back.
Alpha channels have to be enabled.
For lossless alpha channels use floating point. Mute its audio track but keep it playable. Create a new audio track and disable its playback. Attach the new track to the movie's audio track with send and recieve selected. Create a third audio track, disable its playback, mute it and attach a Synthesizer to it with Send disabled but Recieve enabled.