Are there any files inside the archive that may be modified manually? What are the implications?
No file inside the archive should EVER be modified, renamed, or removed in any way.
This includes, for example, the .atmlock file. The existence or non-existence of that file does NOT represent the state of the "lock" on the archive: deleting that file will NOT unlock the archive, and the existence of that file does NOT mean the archive is actually locked.
There's nothing to be gained from deleting that file and if it is done incorrectly then the archive can become corrupted.
Can the archive directory itself be renamed, moved, or copied?
Archive directories should NOT be renamed, moved, or copied unless you are completely sure that no NuoDB process is using that archive (this includes both Storage Managers and also nuochk/nuoarchive).
Renaming, moving, or copying the archive while it is in use can result in archive corruption.