To remove repeated copies so each thing is counted once. Deduplication is how an archive stops lying about its size.
Latin de- (reversal) + duplicare (to double), from duplex (twofold, from duo, two + plicare, to fold); to remove repeated copies so each distinct thing is counted only once.
Its root is doubling undone — duplicare folded a thing into two, and deduplication unfolds it back to one. An archive that has not been unfolded this way is always larger on paper than it is in fact.