The problem does not automatically apply to all projects within a given workspace. However, once the problem occurs for a given project, it appears impossible to make it go away.
Here's exactly what I did to test this scenario out.
1) Made a brand new K24 project "k24_test", selected C, Newlib, all the drivers, mbedTLS, etc.
2) Added the MBEDTLS_CONFIG_FILE define to the preprocessor, since the project won't compile without it (seriously, how did NXP overlook that?).
3) Added our own "secret sauce" headers and libraries to the project, along with the include path, in case there was somehow something in one of those that was causing an issue.
4) Compiled the project successfully. The #include <stdio.h> in the main source is OK.
5) Rebuilt the index, just for kicks. No change, includes look good.
6) Cleaned the project and created an archive of the project in this state.
7) Started copying over a couple of things from my previous project into this new one to see if I could either trigger the problem or manage to completely reconstruct my old project with no issues.
8) Somehow managed to trigger the issue - #include <stdio.h> now appears with a question mark and orange squiggles.
9) Renamed this project "k24_test_indexer_failed". #include <stdio.h> still bad.
10) Deleted our "secret sauce" from the project, which now only contains NXP SDK code. #include <stdio.h> still bad.
11) Closed the bad project, unarchived the "good" project, and re-imported it into the workspace
12) The "good" project now also appears bad, #include <stdio.h> is flagged in orange.
It's #12 that I really don't get... if it were something endemic to the project, I don't see why the indexer would suddenly fail to index standard headers just because I unarchived and re-imported the project.
Anyway, you wanted an example project where the indexer has failed. Ah, apparently I have to use the "Advanced Editor" to include an attachment. See attached. I've added comments in the main source file to be clear on exactly what I'm seeing.