Extending Flash/Bootloader Segmentation induced a bug

Hi Everyone,
Actually, I was making some changes to the bootloader for pixhawk1 (clone), for which I tried to increase the FLASH_RESERVE_START_KB in libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py and libraries/AP_HAL_ChibiOS/hwdef/fmuv3/hwdef-bl.dat from 16KB to 25 KB, but Although Everything works fine, on flashing the copter(from waf) for the first time after mass erasing and uploading bl (through DFU): i.e "

Erase : [====================] 100.0%
Program: [====================] 100.0%
Verify : [====================] 100.0%
On every second upload onwards the .waf command gets timed out upon the erase operation.
Erase : [====================] 100.0% (timeout: 0 seconds)
ERROR: timed out waiting for erase”.
Does anyone have a clue what might be causing that?