Well I'm probably being overly cautious here but its been my experience that if I have a schema that says indexed = true on a field and I change it to indexed = false I have to delete my index to get rid of everything that was indexed with the old schema and I have to restart to be able to index with the new schema.
I've had the situation a number of times where I have changed the indexing rule for a field and not followed these steps and been surprised when my index does not follow my expectations - and it seems like you are experiencing the same thing. Best Regards, Bryan Rasmussen