1. In the hex generated by PSoC Creator buiding, each char character in hex is UPPERCASE, but in the read back hex file, each each char character in hex is lowercase, it won't have influence for PSoC Programmer to decoder the hex file.
2. The difference in the end. The '..' in your hex tool is Line break mark. Actually, At the end of original hex file generated by PSoC Creator building and compiling, there is no line break. But for the hex file read back and encoded by PSoC Programmer, there is a line break at the end. So that this is the reason. For better understanding, you can try using Notepad++ or DiffMerge to compare these two hex files again.
The the UPPERCASE or lowercase format won't have influence on programming and program running.
Regarding the issue you met, I guess it caused by your project. Are there Flash operation in your project, or could you describe more about the issue you met?
thanks, this is a thermostat project and I use ADC, LCD_seg, capsense, eeprom, and uart. Two bytes eeprom should be read and writed， no other operations in it。 While, the AC voltage fluctuation occurs frequently, so the power voltage for cy8c4245 will change。 I guess the hex file in flash could be changed when the voltage raise to a higher value. I use DC5V to power for 4245 in this project.
EEPROM is emulated by PSoC internal Flash, so, if you write eeprom, you write flash. The should be the reason why flash data changed.