This sounds a bit similar to the issue Some objects not readable after batch import / flush and switch failed - Support - Weaviate Community Forum we are having from time to time. Could you try if in your case the affected objects are retrievable when using the same filter as in your delete? Also, it would be interesting if you encounter similar errors in the logs as in that ticket. If possible, also try restarting the Weaviate instances to see if that allows for the objects to be found again as that helped in our case.
Also I saw you are using a very old Weaviate version, is there a reason for that?