Hi,
Please don't take this the wrong way but I would recommend you attend a training class, it will help with some common mistakes you are making. :)
Did you delete the items via EV or just delete the files directly?
Sounds like the index files are still intact, therefore you are able to search still. The best process would have been to delete the archive via the Vault Admin Console, that would have deleted the files and cleaned up the indexes.
Cheers,