How can this be prevented? I think it will be necessary to use thicker metal plates, or even better, several at once, like a sandwich. That is, the main plate with text on both sides is covered by 2 other plates that take all the damage to protect the main plate from deformations and damaged text. The multi-plate construction will have greater rigidity and will not bend like a thin piece of metal.
If a 1000 tonne building falls on your seed no thick metal is going to prevent it from getting damaged it would be damaged beyond repair. It would be crushed and two extra plates even if they were 2" thick would not protect the plate in the middle. Then there is the problem of recovering the plates because you are not the one digging up a 1000 tonne building it will be the emergency services and they will not allow you to go near so they will take that seed or metal not think any more of it and throw it in the trash pits which you have 0% chance of recovering.
The only way would be to remove your seed from a earth quake prone zone.