Did you click Re-Scan or Re-Start the ide after making the external change?

To review issues like this we need the info requested at the top of the forum. This will answer any questions.

Thanks for the output. you also need to switch on the compiler>verbose or I can't see exactly which board and option has been selected. There are some changes to extra flags in your core depending on the board options so I need to see the compiler output.

Thanks

Thanks, we can see the VECT_TAB_OFFSET is correct in the compiler output.

Please switch off "vMicro>Compiler>Shared Cache For Cores". Maybe the core cache is not being release correctly when you changed the extra flags. We will look into it but switching it off should resolve.   

With this option switched off you will have a core built for each project which is cleaner when changing global compiler settings.

If still an issue then then click "Build.Clean Solution" which cleans the project build cache.