Atomic objects don't really work like that. Anyway: use ArrayRules[] to convert to a list of nonzero entries and their corresponding positions, make your replacements, and then convert back to SparseArray[].
– J. M.'s missing motivationOct 28 '15 at 16:48
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This question might be a duplicate of this: http://mathematica.stackexchange.com/questions/13790/using-replaceall-on-sparsearray
– Arnoud BuzingOct 28 '15 at 16:51
ArrayRules[]to convert to a list of nonzero entries and their corresponding positions, make your replacements, and then convert back toSparseArray[]. – J. M.'s missing motivation Oct 28 '15 at 16:48