I've seen similar threads a couple of times now, but not experienced this issue myself yet. One issue I've seen mentioned in this regard is that the flow code can be old and if you set up an S3 lifecycle policy it can randomly delete your flow code. One question from me would be whether it is possible to configure Metaflow to save the code to a separate path to the path used to save data artefacts? I guess that the flow code will be very small in comparison to the data artefacts, so persisting this should not be an issue.