I have the same exact issue with a K60 PCB and Multilink U. We have two custom boards that are duplicates and one of them has this issue. I am wondering whether it has something to do with the chip memory, as in, it has accidentally been locked.
Actually in this case I found that there was problems in how we built the BSP as well as issues in the debugger setup. I do not remember the final solution, but the primary cause was operator error!.
Yeah, I wouldn't be surprised. I think I have to go back and revisit the custom BSP debugger files to make sure it is flashing correctly.