I have a location that I am trying to do a sunset TL. During the Golden Hour, the sky remains bright while the canyon is already in deep shadow. My normal single-still shooting solution would be to use a split-ND filter. But, I'm wondering if I used a split-ND, then pulled it just as the sky reached a luminance c;loser to the canyon area, will the normal processing thru LRTimeLapse handle the adjustments (smoothing the jump, etc.)?

I doubt that you will be able to easily match the shots with and without that filter, since you would have to mimic the exact look of the filter with a linear gradient in Lightroom in order to be able to create a smooth transition.
I'd recommend to shoot without a filter from the beginning. Most sensors today are able to cope with a huge dynamic range when shooting Raw, just make sure to not overexpose.