If you had made any changes to the LDM, it could cause some objects to go missing depending on what had been done. Were any changes previously made
Also, this could be related to how you have set up your
workspace hierarchy, or how you are pushing objects to other workspaces. Could you provide more details if this applies, or are you working with a singular workspace/organization in this case?
As for logs, we can search for a few things, but we would need a time frame and object ID to know what we are looking. Otherwise you would need to create your own logging tool.
As for backups, this is entirely self service:
https://www.gooddata.com/docs/cloud/manage-organization/organization-api/backups/?search=logs