Porting from iccavr project to Atmel studio problems with Atmega2561 8 bit MCU
Atmel Studio uses the GCC toolchain and GNU make. Presumably ICCAVR is using a different toolchain. Your options appear to be:


Keep the ICCAVR toolchain and integrate it into Atmel Studio if you
can get the HEX and ELF files required for programming and
debugging.
Migrate to the GCC toolchain in which case take it slow,
move one module across at a time and test each module as thoroughly
as possible in isolation.