The connection in the toolchain is not being updated properly

I made a toolchain from scratch by looking at tutorial/eigenface/1 . I made some mistakes in connecting the endpoints but at the end I corrected them and all the names and connections in my toolchain were the same as this toolchain. Then I used my toolchain in an experiment but it was not working. It said that the toolchain is not valid because certain connections are wrong. Looking at the json file of the toolchain, it turned out that the correct connections are added to the list of connections without the previous wrong ones being removed from them and therefore the error. I must say that in the beat editor gui everything seemed correct and valid.