I think the replies above are absolutely on-point! I’ll provide a bit of background on this warning for completeness’s sake.
As @peter.cherepanov said, in general it is best to avoid refinements with global pose searches (Non-Uniform and Homogeneous Refinement) with expanded particles. This is because, if half-sets are reassigned, duplicate particles may end up in the opposite set and with the same pose, which would break the GSFSC assumptions and give a spuriously high resolution estimate.
In your case, if duplicate particles have been removed, you are left with only a single copy of each image, so this warning can be ignored, as @olibclarke said. However, the information from symmetry expansion is still there (specifically, the sym_expand fields in the dataset). Therefore, we still present this warning since we do not know that there is again only one copy of each image.
As an aside, this exact case is why we decided to make this a warning rather than fail the job outright.