At first sight, the indexer does not successfully parse the source file you refer to. I noted that you're modifying a relatively large source file (2k+ lines). Maybe this is what's causing the issue? Not sure if there's such a (low) limit though. Would you please try the same use case in other source files and let us know if that works as expected? Anyway, I'd also expect the same behavior in IDE v11.3.x.
You might also want to check whether the "unresolved inclusion" is not reported at all or it's just not shown in the IDE's views (Source and Problems). To do this, right-click the source file with the invalid header inclusion => Index => Create Parser Log File. Then check "Scanner problems" section.
As a side note, CDT comes with a code analysis tool (Codan) and with the Indexer. They both inject markers and they both can be controlled at workspace/project level (Window => Preferences => C/C++ => Code Analysis / Indexer, or via project's properties => C/C++ General => Code Analysis / Indexer / Paths and Symbols). Maybe check these as well.
Greetings,
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