There are many issues with the multi-part Benchy.
I managed to get a fixed version via MakePrintable.com but that fixed file will not work with Slic3r as that slicer requires individual files for extruder selection. KISS on the other hand allows extruders to be assigned to meshes, of which there are 22 in the attached file.
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Please note: I do not have any affiliation with Prusa Research. Any advices given are offered in good faith. It is your responsibility to ensure that by following my advice you do not suffer or cause injury, damage or loss.