Issues with Roto Brushing a clip that’s split into sections

I split up clips all the time. Here's the workflow.

1. Duplicate the entire shot and name the Duplicate Layer "Roto"
2. Add color correction to the "Roto" layer to enhance edge detail and contrast to improve the accuracy of the rotoscoping
3. Split the Roto layers in the timeline (automatically adds a number to the copies) and then extend the outpoint of each clip by 10 to 30 frames
4. Pre-compose the clips, trimming to the clip length and moving all attributes to the Pre-comps, but don't open the new comps*
5. Run Rotobrush on the Pre-composed Roto, Roto 2, Roto 3, and so on layers, freeze, then Pre-compose again, but open the comps this time
6. Go through all of the now open pre-composed and Rotobrushed comps and choose Pre-render from the Composition Menu
7. Run Render from the Render Queue
8. Pre-compose all of the now Rendered HQ movies with Alpha in your main timeline, name it Master Roto, and open the comp.
9. Set up Mat Choker, other channel effects, and opacity fades on all of the overlaps to smooth out the transitions between the layers to create a smooth matte **
10. Back in the main comp, set the fixed, color corrected for contrast Master Roto layer as an Alpha Track matte for the original footage, Pre-compose the pair of layers, and then finish your composite 

* the color correction makes it easier to get good results from Rotobrush and you don't want to clutter up the timeline

** your goal in step 9 is to create a seamless alpha channel to use as a track matte. Switching the Comp Panel view to Alpha Only often helps refine the transitions between the segmented shots

When you have a good matte, go through the Project Panel and delete all of the pre-comps with Rotobrush applied to reduce the AEP project file size and improve After Effects' stability.

I have used this workflow since Rotobrush was introduced. It sounds like more work, but it is more efficient in the long run. The Rotobrush tool in 2025 and the Oject selection tools in the latest version of Premiere Pro have been greatly improved and should make this kind of work much easier and faster. In the few tests I have tried with 10-bit or better original footage, creating mattes works much faster and requires fewer corrections and less need to break up the shots into sections. 

Another workflow hint: Make sure that you pre-edit your effects shots so you don't waste time fiddling with frames that are not going to be used in the final edit. More than 90% of my compositions are less than seven seconds and only one shot because more than 90% of the shots in my edited projects are less than 7 seconds long. That's how all the Major studios work. Pros don't edit in a visual effects app; they use an NLE. Some are better integrated than Adobe is now, but it's impractical to edit a move in an effects or a 3D app.