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[cdt-dev] search for unresolved includes results

I am trying to configure manually (without discovery functionality) indexing of a big C++ project (several dozen K files). Based on unresolved includes I am updating include path entries.
When running "index"->"search for unresolved includes" I am observing strange results: I am getting false indications in some cases. If I open a "problematic" include, it is shown as resolved and I can jump to it using F3. Unfortunately I am not able to reproduce this behavior on small project. Are you familiar with such behavior? Any ideas what could cause it or how to investigate it?
I am using Indigo (CDT 8.0.1).
Thanks a lot,

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