klap-in
If you store a page via the wiki, also a revision stored separately.
So if you delete manually (e.g. via ftp), than if that page is changed(=saved) in the wiki, it will be indexed again. Based on previous versions, metadata and non-existance of wiki page its it will update the changelog and the page metadata to register your manual changes.
If make manually more changes directly after each other, and there was not a indexation trigger of that page in the wiki, the wiki will just see the last state of your manual modifications. And update its changelog and metadata with info of the last version (which is compared to previous known version in wiki).
Tip:
But the simplest manner to see exactly what the wiki is doing and updating is by just deleting, re-adding, modifying a test page and see in the interface what happens. And what happens if you modify it via the wiki editor after a manual edit.
(so the only possibility that the wiki is not registering all changes is by doing a lot of manually modifications to the same page after each other, without that the indexation is triggered in the wiki. All these changes are then summarized as one 'external change'.)
So no repair actions are needed by user or admin.