I’m sorry to say that sounds like permanent damage. I am surprised though… the internal resistance of the voltage input is 10MΩ, so a 1000MΩ probe should divide down the input voltage by a factor of roughly 100 to ~35V, which is very safe. Is it possible there was a source of arcing that cause the meter to be exposed directly to the 3500V source? The meter is designed to measure up to 600V, and fail safely when exposed to voltage up to 4000VAC on the voltage input.
Would you be interested in a replacement meter? I can offer you a 50% off coupon for a replacement, let me know and I’ll send it to the email address you have registered.