@anticimex @Encrypt That's a bit odd and certainly specific to the bootloader you're using (ATmegaBoot): AVRdude does (at least with optiboot) a page erase (vs. chip erase where EESAVE has an effect). I do not have the EESAVE fuse bit set and no issues with erased eeprom when loading a new sketch, also see below:
Arduino Uno with optiboot:
uno.bootloader.tool=avrdude uno.bootloader.low_fuses=0xFF uno.bootloader.high_fuses=0xDE uno.bootloader.extended_fuses=0xFD uno.bootloader.unlock_bits=0x3F uno.bootloader.lock_bits=0x0F uno.bootloader.file=optiboot/optiboot_atmega328.hex
High fuse (0xDE) does not enable EESAVE.