just came across this old post and it seems like we are having the exact same issue.
I created a new software update package for our servers on Tuesday
i patched our DEV servers without any issues.
it is now saturday and we just discovered that the update files have mysteriously been deleted... we have no idea how this happened or why as nobody has been deleting anything.
we blame SCCM for this but its hard to say as theres no indication anywhere as to what is happening.
i know this is an old post but did anybody ever find a root cause for this?