Sorry for the late reply. I was on vacation for the last couple of days. Here is the log and two screen captures to show you the problem.
!SESSION 2017-04-11 07:58:26.579 -----------------------------------------------
eclipse.buildId=unknown
java.version=1.8.0_111
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US
Command-line arguments: -os win32 -ws win32 -arch x86
!ENTRY org.eclipse.ui 4 4 2017-04-11 07:58:44.050
!MESSAGE Plugin org.eclipse.cdt.ui, extension org.eclipse.ui.decorators, id org.eclipse.cdt.internal.ui.CustomBuildSettingsDecorator: Duplicate id found: org.eclipse.cdt.internal.ui.CustomBuildSettingsDecorator
!ENTRY org.eclipse.ui 4 4 2017-04-11 07:58:44.054
!MESSAGE Plugin org.eclipse.cdt.ui, extension org.eclipse.ui.decorators, id org.eclipse.cdt.internal.ui.CustomBuildSettingsDecorator: Unknown extension tag found: decorator
!ENTRY org.eclipse.egit.ui 2 0 2017-04-11 07:58:45.419
!MESSAGE Warning: The environment variable HOME is not set. The following directory will be used to store the Git
user global configuration and to define the default location to store repositories: 'P:\'. If this is
not correct please set the HOME environment variable and restart Eclipse. Otherwise Git for Windows and
EGit might behave differently since they see different configuration options.
This warning can be switched off on the Team > Git > Confirmations and Warnings preference page.
!ENTRY org.eclipse.cdt.core 1 0 2017-04-11 08:00:36.070
!MESSAGE Indexed 'MK64FN1M0xxx12_Project' (0 sources, 0 headers) in 0.002 sec: 0 declarations; 0 references; 0 unresolved inclusions; 0 syntax errors; 0 unresolved names (0%)
!ENTRY com.nxp.mcuxpresso.core.datamodels 2 0 2017-04-11 08:00:37.586
!MESSAGE Overwriting file L/MK64FN1M0xxx12_Project/startup/startup_mk64f12.c
!SESSION 2017-04-11 08:20:48.391 -----------------------------------------------
eclipse.buildId=unknown
java.version=1.8.0_111
java.vendor=Oracle Corporation
BootLoader constants: OS=win32, ARCH=x86, WS=win32, NL=en_US
Command-line arguments: -os win32 -ws win32 -arch x86
!ENTRY org.eclipse.ui 4 4 2017-04-11 08:20:56.338
!MESSAGE Plugin org.eclipse.cdt.ui, extension org.eclipse.ui.decorators, id org.eclipse.cdt.internal.ui.CustomBuildSettingsDecorator: Duplicate id found: org.eclipse.cdt.internal.ui.CustomBuildSettingsDecorator
!ENTRY org.eclipse.ui 4 4 2017-04-11 08:20:56.343
!MESSAGE Plugin org.eclipse.cdt.ui, extension org.eclipse.ui.decorators, id org.eclipse.cdt.internal.ui.CustomBuildSettingsDecorator: Unknown extension tag found: decorator
!ENTRY org.eclipse.egit.ui 2 0 2017-04-11 08:20:59.617
!MESSAGE Warning: The environment variable HOME is not set. The following directory will be used to store the Git
user global configuration and to define the default location to store repositories: 'P:\'. If this is
not correct please set the HOME environment variable and restart Eclipse. Otherwise Git for Windows and
EGit might behave differently since they see different configuration options.
This warning can be switched off on the Team > Git > Confirmations and Warnings preference page.

This screen shows that I have MY_TEST variable defined. Since the .cproject file is read only, the setting is not saved. I think the tool should at least warn the user about it. But I never got any warning about it. After I quit the tool and relaunch it, the setting is gone as shown below.
Again my question is not about read/write access, my question is about if settings can't be saved, why the tool does not warn user about it?
