Hello,
You had asked "does EV ever touch/re-archive them again automatically"
Just to make clear; the message is not re-archived again since it was already archived once. Yes, the message goes to 'archived' as a shortcut but EV knows the messages (using the hidden information on the message) and does not archive the message again in the vault. EV simply removes the message from the Exchange server again. As you had said, yes "that item (is) flagged".
For instance if I archive a message, then search the vault I find the one message. If I restore the message and archive it again my search will still only find one message.
This is because the message, when restored, has hidden attributes that EV can use later when the message is archived again.
As the poster above had said, yes EV archives based on modified date.