When You have a project that sets:
Properties -> Debug -> Flash Settings,
the flags that are selected in the original project are not taken over in the copy.
These flags were different after my copy:
System Reset on Connect (on in original, off in copy)
Auto ECC Generation (off in original, on in copy)
Flash Verification Settings (None in original, Verify in copy)
No big issue, just a heads up that this is happening.