Many people have reported that the include paths are being deleted in the project. I haven’t worked out how/why/when this happens yet, but suspect it is something to do with different tool versions or tool installation directories.
The easiest way to add them back in is as manual command line options. To do this, bring up the project properties dialogue box, then go to Configuration->XC32 (Global Options)->XC32-GCC category. You will see a “Additional Options text box on the right side. In this box add the following text:
-I ../../../Source/include -I ../../../Source/portable/MPLAB/PIC32MX -I ../../Common/include -I ../
Do the same for the XC32-as options.
Let me know what happens.