Github repo cannot be clone after some time with error "Repository not found"

This indicates the github oauth2 access token is being revoked or is no longer valid. These are the only known root causes for the issue that you have described:

  1. the user that activates the repository has their repository (or organization) access revoked. Drone clones the repository on behalf of the user that activates it [1]. If the user no longer has access, Drone will be unable to clone the repository.
  2. the user that activates the repository revokes Drone’s oauth application authorization (via the github settings screen)

[1] Does Slack plugin still support status: change? - #2 by ArturGajowy