Eclipse CDT - "Program "-E" not found in PATH

I had quiet similar problem, in my case changing toolchain from Linux GCC to Cross GCC in project properties (C/C++ Build -> Tool Chain Editor -> Current toolchain) resolved the issue

In the project settings go to "C/C++ Build > Tool Chain Editor". The selected tool chain was empty in my case. Thus I selected the tool chain that I use (which seems to be "Cross GCC" in your case). This will set the ${COMMAND} variable (and ${FLAGS} and ${INPUTS}), which seems to be unset in your case. If you for example close the project and reopen it the error should be gone.

The second option I see is that the command with which Eclipse determines the default definitions and include paths of your compiler/tool chain got screwed up when you "tweaked your project". You should be able to fix this as follows: Open the project settings and go to "C/C++ General > Preprocessor Include Paths, Macros etc.", select the "Providers" tab, select the active "CDT * Built-in Compiler Settings" provider from the list and make sure that the "Command to get compiler specs" starts with '${COMMAND} -E' instead of '-E'. In my case the complete line is '${COMMAND} ${FLAGS} -E -P -v -dD "${INPUTS}"'. If you no longer want to see the output when Eclipse is executing this command you can uncheck "Allocate console in the Console View".