bratan:
If you interested in uploading sketch without loosing Bootloader use this command:avrdude -C c:\programs\arduino\hardware\tools\avr\etc\avrdude.conf -patmega644p -cavrisp -P\\.\COM5 -b 19200 -D -Uflash:w:yourhexfile.hex:i
No this will not work correctly from ISP programming. You will see it will not work once you change your program. Try adding a line to you code and then re-upload it with that command again. It will probably not work anymore.
The flash memory cannot be programmed to back to a "1" once it is programmed to a "0" unless you erase it. The -D option only works with a bootloader because it does a page erase at a time instead to reprogram. If you reprogram via ISP then the only way is to erase all flash first.