was the file distributed prior to your change or after?
I have found that if the change is made after, it does not go back and clear out old files. I believe as each file is cached it is time stamped at that point and will die when it expires.
Now that I think of it, it may have been after. What I did is setup a distribution package setting the main file as the batch file, with the .reg key and office 2003 files as "additional" files. What originally happened is the Office files and batch file copied over to cache, but the .reg key didn't make it so the batch file failed and the registry never updated. I reset the hash on the .reg key, ran the task again and it succeeded in changing the registry, but to answer your question I guess technically the files were already there before the registry change. Do you suggest I just manually delete all files out of cache, set the registry back to the way it was, reboot and rerun the whole task again?
If this on one machine, or just a few, manually deleting it would be the easiest.
If have a lot of room on the hard drive, you could just wait for it to expire normally.
If you have a lot of machines with it and you need the to free up space, you could send a script to delete them, otherwise again, you can just wait the two or 14 days it takes to expire.
BUT.... If you want to the same files to be on the system for a deployment, you can just rerun your task and those that are there will just be checked to ensure the hashes match and anything new or different will be downloaded as needed.
Not exactly sure what you are doing, so that it why I offered so many choices.