You cannot just delete files to remove an index from a server. This will leave the search service corrupted. Use the following steps to remove an index (replacing index_name with the name of the index you wish to remove):
/usr/IMNSearch/bin/itedelix -s server -x index_name
/usr/IMNSearch/bin/itedomap -p /var/docsearch/indexes -d -x index_name
rm -r /usr/docsearch/indexes/index_name