actually the HAL_Delay() function cause, as it implies, a delay. In case of delaying a too long period, the Embedded Wizard update routine cannot refresh the UI often enough. This could look like a freeze, but technically it isn't one. I suggest in your case to use a (FreeRT)OS, to guarantee that Embedded Wizards update cycle can run without beeing delayed by the HAL_Delay() function.
As you already have figured out, your new application and Embedded Wizard probaply runs within the same loop. Thus you have to take care about that applications do not block each other when you're using the HAL_Delay() function.