Question

Will changing the Active Directory account name affect their ability to use the FlexiCapture application?

Answer

The only way this would only affect Flexicapture is if the new AD username is changed and doesn't have the same permissions when logging into Windows.  Flexicapture works off the currently logged-in user account.  

If you are importing the AD info for user accounts directly into Flexicapture, you would only need to verify that the new user account has the appropriate permissions in the Admin & Monitoring console

Additional information

Using the Active Directory to manage users