Just for ref, after abit of experiments overwrite Append 1 worked great on my side like this:
Open FDSE "Source.bin" 9 # Open source file you want to overwrite data in, refer as "9"
Get S_SIZE asize 9 # Get source file total size as S_SIZE
Get I_SIZE asize # Get input file total size as I_SIZE
Log MEMORY_FILE 0 S_SIZE 9 # Place the whole source file in MEMORY_FILE
Goto 0x20 MEMORY_FILE # Which offset to store input file
Log MEMORY_FILE 0 I_SIZE # Input file starting offset & size
Log NEW.bin 0 S_SIZE MEMORY_FILE # Log to new file
Of course, by repeating the "Goto -Append 1 - Log - Append" chunk, you can overwrite to multiple offsets at once.