I have noticed a few bugs in the IDE, but I couldn't find any place to report it, so I'm reporting it here.
1. Change memory settings in "MCU Settings".
2. Press "Apply".
3. Press "Apply and close".
4. Check .cproject file. The new settings are not being persisted.
If you skip step 2, the new settings are correctly being written to the .cproject file.
There is no way to trigger MCUXpresso to save the new settings now and they will be lost after a restart or open/close of the project.
This is valid for at least MCUXpresso 10.2.0, and 10.1.1.