[~manthos], thanks for the test case. I extracted a test case which runs in our test suite - https://github.com/hferentschik/hibernate-search/tree/HSEARCH-1358 - and I can confirm the problem.
It seems the issue is actually caused by an ORM problem. In the test case updating the categories map does not trigger an update event for Search. This means there won't be any re-indexing at all. I'll need to find out why the event is not occurring. Most likely a fix in ORM will be required to address the issue.
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