Moved topic to coresponding sub forum CODESYS - PLC Add-ons.
So you really are changing the configuration of ther EterCAT fieldbus? Or how do you switch between the topologies?
EtherCat can actually not perform any hot plug functionality and in the actual state will give addresses automatically depending on the topology. See online documentation.
You can switch up the EtherCat partially to OP and not all modules need to be attached. In standard all data is transmitted in one package and as soon as one datum is faulty all data will get invalid. But several data packages can be set up that are checked individually. This is handled via so called "sync units" (see docu). So if a missing slave is another sync unit then the rest, the bus can go up.