Hi,
I noticed two related issues on MCUxpresso:
A) If there are linker scripts (LD files) in subfolders of a project, they are parsed even if the folders are excluded from compilation (IDE's "Exclude from Build..." feature). This generates IDE errors even if there are no compilation and linker errors. In the errors tab you can read "GNU Linker Script Problem" for each LD file present.
B) If the IDE reports an error, the GUI Flash Tool functions are rejected with a message box that says: "Operation not completed!". But in reality nothing happens, it doesn't even try!
If I delete the folders containing the LD files or the individual LD files, everything works fine.
I attach an image where you can see the error report on the folders excluded from build, the errors tab and the GUI Flash Tool message box.

Thanks
Marco