You could use RTWE to clear the space as well, by typing "FFF1" as a text (without the quotes) above the head.
FWIW, I use codemanager (PC application) to convert the codes from text file format to gct file format, and it always works fine for me. Do you have other codes in addition to RTWE in your ACCF gct file? If you could share your codes (in the text file format), then I could perhaps try to see if there is anything wrong about it. One easy way to check whether the problem is with your current RTWE code or not is to remove all other codes and just use RTWE and execute the same steps as you did and see whether the town has those invalid items or not after that.
Hope that helps.