There are two ways to remove documents from an index: 

(1) You can pass a list of filenames to be removed from the index in an index job. The list is passed as a plain text file containing a list of filenames or DocIds, one per line.  Filenames must exactly match the path and name associated with a document in the index.  DocIds must be preceded by > to indicate that they are not filenames.  Each item must appear on a separate line.  Examples: 

c:\docs\filename.txt 

>45 

This list would specify that the document "c:\docs\filename.txt", and the document with the DocId 45, should be removed from the index. 

(2) You can set the "Remove Deleted" flag in an index job, which indicates that each file in the index should be checked and, if the corresponding disk file does not exist, the file is to be removed from the index.

Building and Maintaining Indexes