They would have to put them back to agents that are fired or resign. Also, it would be noticeable for police that in some crime scenes there people without fingerprints, It would be better to change their fingerprints for other finger prints
The stupid have one thing in common.They alter the facts to fit their views not the other way
In the comics on which this movie is based on agents don't retire. Once you join it's for life so death is the only exit, either self inflicted or by the hands of the agency.
For the "kid friendly" movie version I'll bet they just looked over this part. As for a movie explanation, I'll bet they have an alien gizmo to put fingerprints back or even print new fingerprints incase an agent does not want to return to his previous identity.
My guess is that if you have to do the de-fingerprinting procedure every 4 weeks, you probably wouldn't feel anything anymore after a few months. After all it only takes a few seconds, in return you get a world of endless wonder.
And in the M.i.B. universe there is no such thing as overthinking something.