Polybrush won't save to prefab

I'm working on a low poly game, and I built a custom shader for wind on trees. I need some kind of mask to block the effects on the trunks and general unmovable parts. I came into the project part way through, and the game's UVs are set to a color grid texture, so none of the objects have UVs that are usable for much else. I thought poly-painting would be a great way to generate a mask without re-UVing all the foliage assets.

I used polybrush to paint a mask onto all of the assets and it looks beautiful. Only problem is, when I applied my changes to the prefab, it didn't save any of the polybrush data, and none of the assets in the other scenes were updated.

I've made copies of the painted assets within the scene, and the polypaint data is preserved. I've closed the scene and the project, then re-opened it, and still, the originals I painted worked fine, so I know the data is being recorded, it just isn't being applied to the prefab.

All this is made worse by the fact that despite the tutorial videos claims to the contrary, polybrush doesn't appear to have any online documentation (none that I can find at least). So if anyone has a link, that would also be appreciated.