What does the prophecy mean?

Basically it means that the future will be destroyed in the past, and the past will be saved in the future; namely, the Metal Men came from the future to take the petrified people of Gandahar to feed Metamorphis, and it is there where Sylvain kills Metamorphis as well.

Here is what I think:

Lets make some simple time references:

Now, the present, is the specific time of the beginning of invasion and the conquest of Gandahar. This is the same time in which Sylvain was sent to his mission and meets the mutants for the first time.

Future - is the time in which the Metamorphis is dying, he creates time portal and sends his troops a thousand years back to start taking the Gandaharians.

The prophecy:
In a thousand years Gandahar was destroyed - means that in the future certain events will take place that will destroy current Gandahar. This is of course the opening of the time portal and the invasion. The reference is twisting the language because it refers to both Now and Future as the same. It is quite logical, because time portal makes both points in time to exist together.

A thousand years ago Gandahar will be saved - this is of course reference to the events, in which Sylvain was put in stasis. The reference is from the standpoint of the Future. By putting Sylvain in stasis and asking to kill him in thousand years from now, Metamorphis is saving the Gandahar. From the future it looks like thousand years ago Gandahar was saved.

The confusion created by the prophecy is purely linguistic. The seeming paradox is not paradox at all. This is just linguistic nonsense, and quite simple one once you saw the whole movie.

All people in the statue head that were taken by the birds, probably went to some remote place in the mountains or something, where the robots will not find them. It is not really explained, mostly because it is not that important.

Hope this helps.

When he enters the future Gandahar is gone, but when he returns to the past it is now safe.

Simple enough, but cryptic because the order seems wrong when first heard. But that is the sequence and times of the events of the film even though the grammatical tenses remain messed up.

Keeping in mind that the Deformed was/shall be bad at grammatical tenses.

In a thousand years Gandahar was destroyed ( I think that refers to the main character having to fight the villain in the future); a thousand years ago Gandahar will be saved.(That refers to the people of Gandahar being saved in their present by the actions of the hero in the distant future battle). As time travel is involved you can have a situation where the past is saved by actions which the hero has yet to take in the future. If I travel from today into the past then the past becomes my future while from the point of view of those in the past my past is their future. So let's say I went to late June 1969. To me the moon landing is the past (in fact I wasn't born til about 18 months later) but to people who were living at the time the moon landing was still an event yet to happen. So my past is at the same time their future and their future is my past.