A single chunk 'should' not erase a whole ship.
The 'search' is a good try, it may got displaced somehow.
Were you playing single player mode?
You should always create some backups of your client folder, or at least and for ships totally fine:
Blueprints (but use: save in local catalog, in this case its saved in a separate folder), then you only need to backup the folder it created with the same name as the blueprint)
- Andy