Hello,
First of all, sorry for the late reply.
If you reset the evaluation board while FreeMASTER is already connected to the board, you have to STOP the FreeMASTER connection and start it again. Otherwise, it is going to get stuck.
One way I do what you want to achieve is to store the state of the LED in a Data Store Memory. Apply the NOT operation (to change from LOW -> HIGH and HIGH -> LOW) and feed the value to Dio_WriteChannel. This way, you can mark the Data Store Memory as Volatile or External so you can load it into FreeMASTER project.
If you want to be to perform the read and write operation on a DIO channel, you need to configure the pin to be configured as INOUT (Pins tab in S32CT).
Best regards,
Sorin Bancila