Practically, how were rebels identified and kept off the ballot. What happened if one ended up on the ballot anyway?
Only certain senior officers and Confederacy politicians and officials who were relatively well known were specifically excluded from the franchise under the Reconstruction Acts. Otherwise, the states that had seceded and joined the Confederacy were placed under federal, military rule during Reconstruction.
So there was no requirement by law to identify all former rebel soldiers who might have moved anywhere in the USA and stop them voting.