We recently came across this issue, we wanted to clean up our old indexes and build our environment. We rest the index from SharePoint and FAST server and did a full crawl. We observed that after the crawl is complete there were no data being retrieved in our searches. On looking further we observed that the FASTSearch conetnet collection and crawl logs are indicating that all the data has been crawled and indexed.
We performed an incremental crawl and amazingly we got some of the data searchable i.e. whatever data was re-crawled was not retrievable. Looking at the indexer info we got something similar to below details:
<documents size="26854297742.000000" total="XXXXX" indexed="YYYYY" not_indexed="ZZZZZ"/>
Here XXXXX = YYYYY + ZZZZZ.
This clearly showed that there were some issue with the indexes. We needed to re-index the data to get the issue fixed. we used the below command for the same: