Which core module? Does your program ever write to the flash (perhaps the UserBlock area?)
To what extent has it been erased? If you have a module that's failed, can you try using the "extract_flash.c" sample (link below) to download a copy of the full flash contents, and compare that to the expected .bin file to see if it's the entire flash, or just a critical area (e.g., the first page) that's been erased. Or maybe it's not an erased page, but a single bad byte?
The Windows app "Beyond Compare" is good at comparing binary files.