Edit: Nori posted reply #3 while I was still typing the text below. So the problem seems to be the file size and not what I had guessed.
The problem might be this: For the transfer to work, the save file that exists on the Retrode must be overwritten "in place": Open file X, overwrite data, close file X.
Your PC might instead be trying to create a new file Y, fill it with the data, close file Y, delete file X and finally rename file Y to X.
The latter does not work with the Retrode. It fails in the first step (create new file Y) because there is no free space. The Retrode has not enough memory to buffer a temporary file, and it cannot tell where else the data should go (config? save? ...).
Please try the following and tell us if it worked:
First, check that the save file on the Retrode is exactly the same size as the save file that you want to copy over.
If the sizes match, "delete" the save file on the Retrode. This will only remove the file's directory entry and mark the area where the file is mapped into the Retrode's virtual volume as free. The actual save on the cartridge will not be harmed.
Finally, copy your new save file to the Retrode. This should cause the PC to write the data to the proper area.
Warning: In the time between deleting the Retrode save file and copying the new one, do not edit anything else on the Retrode.