I am using NXP_MBDTToolbox_MPC57xx version 3.2.0 with R2020a. I am using the X-RDVCU5775EVM dev board which has the MPC5775B chip.
I have created a simple model to demonstrate the problem. All of the blocks are shown in the image below.

The input pin for the GPI Read block is "PTG4: [SIU_A_GPIO196 | General Purpose I/O 196]" and is shown below.

The model works as expected: when a board GPIO circuit is closed a board LED lights up. However, the problem occurs when I save the model and reopen it. When I reopen it the blocks look look like this. Question marks appear on the GPI Read block mask. That is not the expected behavior.

When I double-click on the GPI Read block the question marks are replaced by some text and an pin assignment is made that is not in agreement with the pin assignment I made before the file was saved.

This is probably a bug. The behavior I expected was for the pin assignment I made before the file was saved to persist after I closed and then reopened the file.
I have attached my file. A fix would be appreciated.