Solution
Yes, we can use System Exec.vi to execute a command that expects multiple inputs. Take for example the Python script below that expects two user inputs in a single execution.
def get_user_choice():
while True:
user_input = input("Please enter 'Yes' or 'No': ").strip().lower()
if user_input in ['yes', 'no']:
return user_input
else:
print("Invalid input. Please try again.")
# Usage
choice = get_user_choice()
print(f"You selected: {choice.capitalize()}")
choice = get_user_choice()
print(f"You selected: {choice.capitalize()}")
Notice that this script is calling get_user_choice() function twice, so the user must enter "Yes" or "No" or any other string at least twice for this script to end execution.
A manual execution of this script in Windows Command Prompt would yield this result:

In order to yield the same result in LabVIEW, we can use System Exec.vi and wire the user inputs to "standard input" terminal with a line feed (\n or ASCII 0xA) in between each input.
Note: This image is a LabVIEW snippet, which includes LabVIEW code that you can reuse in your project. To use a snippet, right-click the image, save it to your computer, and drag the file onto your LabVIEW diagram.
When the VI above is executed, you should get the following result.
