In future episodes, all characters--Julia, Barnabas, Elizabeth, etc.--refer to him as Eliot Stokes even though he currently goes by Timothy. I always felt that the writers had grown careless when they made the change. His full name is Timothy Eliot Stokes.
Unless I'm mistaken (which I may well be) the character was introduced post 1795 as "T. Eliot Stokes." I have heard Julia refer to him as and call him Eliot but I have not heard anyone mention the name "Timothy."His counterpart in parallel time, when we get there, is called Timothy Stokes, father of Alexis and Angelique. That is the only time I recall anyone using the name Timothy.