Try projecting at a slower frame rate, there are many variable speed super 8 projectors that could project at rates like 12, 9 or 6 fps. Your camera also might be able to shoot at a rate that could matchthe slower projector speed. IIRC there was a British filmmaker whose name escapes me, active in the 70s and 80s, who shot and projected his films at 6 fps.
You could also try modifying the shutter blade on the projector. Its not my area of expertise but I think that if you had fewer shutter blades that you would get more flicker.
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