Cannot rotoscope entire scene - processed frames are being removed - 25 sec clip

Rotobrush is not a magic one-click solution. If you need to rotobrush a clip start by trimming the clip in the Footage Panel and then create a Roto Comp from the trimmed shot. Trim the shot to include only the frames you need to use in the final edit. After trimming the shot, you should add masks to simplify the roto if possible. You should also use color correction and even sharpening to improve edge contrast and detail if necessary. When the clip has been trimmed and prepared, you should Pre-compose the shot, moving all attributes to the new comp and trimming the comp to the layer length if it is shorter than the Roto comp. 

After Pre-composing the layer in your Roto comp, run Rotobrush on the nested pre-comp. When Rotobrush has finished, and you have done all the cleanup, freeze Rotobrush, then make final adjustments and cleanup using the Effects Control Panel. 

The color corrected and masked, if necessary, pre-comp should be the only layer in your Rotobrush comp. If you spent more than a few minutes doing the roto, you should choose Composition/Pre-render from the menu to render the Rotocomp and import the footage with an alpha channel. The goal to this point is to create a layer with transparency that you will use in the Main comp to complete the composite. 

Rotobrush bloats your project file size, is incredibly taxing on system resources, and can be unstable, so it is almost always a very good idea to render the Rotobrush comp, import the footage, then delete the Rotobrush comp from the project. 

If you really need all 25 seconds of your shot as a single take, you may have to split the shot up into several shorter segments, then combine the rendered Roto comps in a new master comp for the compositing. 

For the final composite, I almost always use the rendered Roto footage as a track matte instead of source footage. If I need to use the rendered shot as a source, I always turn off any color correction that I applied in the pre-comp after Rotobrush has been frozen and final adjustments have been made. 

I hope you followed that workflow. Rotobrush is a useful tool, but it is not magic and the footage must be shot with Rotobrush in mind. Let me repeat this suggestion. Any time you spend more than a few minutes on a Rotobrushed shot, you should render the comp and delete it after you get a successful roto. It is almost never a good idea to include a Rotobrushed layer in a comp with a bunch of other layers to complete the composite. At the very least, pre-compose your frozen and locked Rotobrush layer before adding other layers to the main comp. 

I hope this helps.