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Ana results conflicting

I have had symptoms for years & was dx with UDCTD but I recently had 3 months of a flare. I had labs done again that had a positive direct Ana , positive anti-smith, c3 80, but IFA said negative ANA. At the time I was on plaquenil for a month & flare was resolved. Does anyone know why IFA would be negative & the ana direct positive? Is this Lupus? During flare I had terrible dry eyes ( for plugs put in ), swelling eyes, face, hands & legs, joint pain everywhere & severe fatigue.
Thank you for any info
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