Is anyone else seeing the same issue where Content Indexing stops working and needs to be manually flushed?
I believe I have narrowed down the root cause for our instance - whenever Confluence loses access to the database (e.g. we just had a database outage so routine maintenance could be made), on restoration most of Confluence appears to work fine but Content Indexing is broken. Same happened for last maintenance window. Only fix that I have found is restarting Confluence.
I had the same issue a couple of months ago. Not sure it was related to a lost database connection...
At the time it looked like a problem with attachment indexing. That's what the logs said. Did you check your logs?
Restarting did solve the problem but it came back after a while. After a Confluence upgrade I never encountered the problem again. Are you on the latest version?
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