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What you could do is keep the RenderTargets and Viewports for both textures at all times, but then you set the rendertargets to active or inactive depending on the current frame, e.g.
# for an even frame
rendertarget0->setActive(false);
rendertarget1->setActive(true);
# for an odd frame
rendertarget0->setActive(true);
rendertarget1->setActive(false);
Hi scrawl, thank you for your reply.
That is along the lines to what I did. However I duplicated everything, including the Compositors and viewports
Then I swap everything and trigger the viewport update alternatingly after every update.