Best practice for deleting Entities with data and Journals

Hi
we are trying to create a subset of data in a new application, by copying the main application and then deleting the entities we no longer require, however these have data and journals posted, when loading the metadata and the Check integrity box is checked the new metadata fails to load due to the journals. can we simply un check the Check integrity box and load metadata followed by a clear invalid records? or is the only way to delete the journals first?

Thanks
Sarah