Attempting to package a runtime plugin (does not occur with a Development plugin) in a Blueprint project fails in 4.21 Preview 2. This also causes some Editor files to be deleted, including the Modules file. This results in the editor crashing on launch.
This only occurs in Binary builds of the editor
Verifying the installation of the editor fixes this issue.
This did not occur in 4.21 Preview 1
This has not been currently tested on Main, I'm currently in the process of retrieving a Main binary to test with.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-65595 in the post.