Do you know what kind of flatworms they are? Some are resistant to it, but you may consider using flatworm exit on the 3 gallon. Otherwise, if you don't want to introduce them I wouldnt combine the tanks.
read up on flatworm exit. I'm not sure how you'd dip all the inhabitants of the 3 gallon to get rid of the worms, but in an-tank treatment of FWE should do the trick.
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