On a atmega2560 the usable flash is meant to be 256k-8k bootloader. Ie 0-0x3E000 (253952 bytes.) but in the code is

#if FLASHEND > 0x0F000
	#define BOOTSIZE 8192
#else
	#define BOOTSIZE 2048
#endif

#define APP_END  (FLASHEND -(2*BOOTSIZE) + 1)

FLASHEND is 0x3FFFF on mega2560's so the the BOOTSIZE is set to 8192, but the APP_END is set to (0x3FFFF - (2*0x2000)) + 1 = 0x3C000

The code then uses "if (eraseAddress < APP_END )" so uploading over serial will only erase bytes from 0x00000 to 0x3C000. So 0x3C000--0x3E000 is not erased and can't be reused till a full erase is done.

This has been causing headaches for years.