I deleted and updated multiple items in one of my categories. Previously, I had 20+ items across 3 different brands in my category. I deleted a number of them and now have 14 items across 2 brands. However, when I go to that category, it still shows "26 Item(s)" at the head of the results, and the layered nav still has product counts for attributes from the delted products. For example it still lists the brand that has been deleted completely as being returned with (6) products. If I then click to filter by it, no results are listed as the items have been deleted. I am assuming it is a caching or indexing issue but my indexes all show up to date and I have flushed and refreshed the cache.
EDIT: Update and some more information:
When I reindex catalogsearch_fulltext, it fixes the item counts. HOWEVER, it then causes many of my items not to show on the site any longer. So now the category will show the proper count of 14, but only 4 items will show up. The items still exist on the site and their item detail pages can be accessed directly, but they don't show up on list pages. This appears to only happen to items added somewhat recently. I am still pinpoiting the exact product ID that is the cutoff, but all after that cutoff fail to show on a reindex, but all before still show on a reindex.
To try to fix it, I disabled and re-enabled all items in the category, which caused them to show again. However, when I then did a mass disable/re-enable on the rest of the site, some items went missing again. I had to go through each category and do them that way to get them all to show again, but the counts are now off again as well.
Some relevent configuration info: there are two magento instances on the server, and running the indexer on one instance also runs it for the other, and I'm not sure why that is the case. They are configured for separate databases. The site also uses a SOLR instance running on the server.