An easy way to move all your geometry files where you want them without having to edit CR2's. Move all your geometry files (.obj) anywhere you want them in the geometries folder. Then run Correct Reference. Correct reference will re-assign all the geometries correctly in your CR2's. I moved over 3000 obj files around and renamed all the folders, ran Correct Reference once, and problem sorted. Same for textures. The only problem arises when there are two files with the same name, like black.jpg, then you have to manually choose which one in Correct Reference.

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