Shouldn't do - after all it is the FBoot boot loader that works on the CPU to receive and re-burn the flash. If anything is overwriting the boot loader then it can only be the boot loader itself that is allowing/doing it. Webbotlib Studio cannot 'write' anything directly - it can only talk to the boot loader. Suggest that either the bootloader is at fault or perhaps the fuse settings that protect the boot loader.
More info re board, processor, hex flash size, fuse settings, fboot version etc may help. But it ain't Webbotlib Studio !!
I hooked up my avr dragon device programmer and checked the fuses. They are set correctly as specified in SoRs Q&A section on fuses.
One thing I did notice is that when it works the first time, there is a "[INFO] AVRISP MKII (avrdude):..." message that is output to the Webbotlib Studio "Output" window.
However, that message does not get output during the second attempt that fails.
What I don't understand is even though I set "Programmer:" to "Fboot", why does the "[INFO] AVRISP MKII (avrdude):..." message get output? I'm not using an AVRISP MKII.
First attempt (success)....[INFO] Flash: Start
[INFO] Flash: Regenerate project with earlier settings
[INFO] Flash: Regenerate the makefile
[INFO] Flash: Clean and compile sources
[INFO] Flash: End
[INFO] Flash: Project has been regenerated and compiled ok
[INFO] Flash: Upload file is called:walle_robot.hex
[INFO] AVRISP MKII (avrdude): com.webbotlib.studio.programmers.avrdude.AvrIspMk2AvrDudeFlasher add mapping for processor:ATmega640=>m640[INFO] FBoot: Parsing file walle_robot.hex
[INFO] FBoot: File contains memory segments:
[INFO] FBoot: 00000-024BD
[INFO] FBoot: connected to COM4
[INFO] FBoot: Start Flashing via COM4 at 115200 baud
[INFO] FBoot: Switch on your board
[INFO] FBoot: Trying to connect...
[INFO] FBoot: ...Connected
[INFO] FBoot: Check CRC support
[INFO] FBoot: Bootloader V2.1
[INFO] FBoot: Signature: 1E9608
[INFO] FBoot: Buffer Size: 7168 bytes
[INFO] FBoot: Maximum Flash Size available: 64512 bytes
[INFO] FBoot: Check CRC support
[INFO] FBoot: Checksum is OK
[INFO] FBoot: Start Programming
[INFO] FBoot: End of block:7168
[INFO] FBoot: Block programmed ok
[INFO] FBoot: All data processed
[INFO] FBoot: Start Verifying
[INFO] FBoot: All data processed
[INFO] FBoot: Check CRC support
[INFO] FBoot: Checksum is OK
[INFO] FBoot: End Flashing - OK
[INFO] FBoot: disconnected from COM4
Second attempt (fail)...[INFO] Flash: Start
[INFO] Flash: Regenerate project with earlier settings
[INFO] Flash: Regenerate the makefile
[INFO] Flash: Clean and compile sources
[INFO] Flash: End
[INFO] Flash: Project has been regenerated and compiled ok
[INFO] Flash: Upload file is called:walle_robot.hex
[INFO] FBoot: Parsing file walle_robot.hex
[INFO] FBoot: File contains memory segments:
[INFO] FBoot: 00000-024BD
[INFO] FBoot: connected to COM4
[INFO] FBoot: Start Flashing via COM4 at 115200 baud
[INFO] FBoot: Switch on your board
[INFO] FBoot: Trying to connect...
[INFO] FBoot: Timed out
[ERROR] FBoot: Error during connect: Timed out
[WARN] FBoot: End Flashing - FAILED
[INFO] FBoot: disconnected from COM4