Yes. You can use SSIS data flow for this. You need a package with flow as below
1. data flow task with flat file source connecting to flatfile
2. Lookup task to lookup wuth table on old values. Set lookup failure action as redirect row to No match output.
3. Join Match output to OLEDB command and write update statement to update oldvalues with new ones
update query would be like
UPDATE Table
SET FieldName = ?
WHERE FieldName = ?
and map 0 to new value and 1 to old value in parameter mapping tab
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