Thanks for the reply.
So, yes, the API seems to not return some items where status = 3 and the filter object I use with the list method of the baseEntry object has the status property set to DELETED.
I should have been clearer. I am setting the Filter for the API calls to return deleted entries specifically. You're right in that they API won't return deleted entries without setting the filter for Deleted entries.
I might try running the Sphinx script to see if that solves the issue. Are there any potential issues with running this script on an otherwise functioning system?
I noticed there is a column in the entry table display_in_search. I can't find what this might correspond to. Do you know? I can't find much documentation on it.