In the system you have to reconcil the checks one at a time. Then you can purge the data for reconciled checks in a range by date of check number. If I was in your spot, I would do what you mentioned. I would use a sql update script to flag the checks as reconciled. Before running the script, I would backup my database, then fire away.
Then you could use the natural system to purge. I always figure the level of harm ranges from select (minor), update (major), insert (dangerous), delete (never do - unless gun to the head).
I would update the checkrec_sql file and set recon_dt = 19800101 where chk_dt < 20040101 (You would set this date) and recon_dt is null (this is optional).
Note I have given you the sql to update the data, but you would have to know sql to piece back togther. I didn't think it was a good idea to dirrectly post an update script.
If you know SQL you can put it back togther then you own the script, and the effects there of.