If the assets in your new server retain the same qualifiedName, then these will be recreated in Atlan with all the metadata attached. The qualifiedName determines asset uniqueness in Atlan (and influences the GUID of the asset). Following this logic, any asset recreated with the same name will remain the same asset in Atlan — considering that the qualifiedName has remained the same.
By contrast, if an asset is recreated with a new name, it would become a new asset in Atlan — considering that the qualifiedName has changed. This means that the attached metadata will no longer be available.
If an asset is removed from the data source or no longer available, it will be archived in Atlan as part of the crawler's cleanup policy.