If you do not currently have access to a DBI compatible database you may want to look at using DBI and the DBD::CSV driver with your flatfiles. It will handle your file locking (assuming you're on a system that has flock()) and will allow you to take advantage of the ease of use of SQL when performing your operations.

Then, when your project outgrows the use of flatfiles and you simply have to move it to a real database, porting the scripts should be fairly easy, since you built it around DBI from the start.