Okay, since you've made this public I'm going to post my results here.
I've been experimenting but I'm going to call igazor in here to make sure I'm on the right track.
Start with a clean install (take your Electronic Arts folder out and place it somewhere else, then open the launcher to generate a new one) then transfer your store content and saves over to the clean folder. Transfer only the EBC files, not the DBC files! The DBC files are custom content. Putting your saves back in to the clean file should not reinstall the counter. When you open the save that had the lot with the counter it should be replaced with a base game counter I think?
Then any cc you want to keep, use the S3P extractor to turn it into a package file and put it in your mods folder. Don't install through the launcher!
Calling the expert who scared his neighbors by screaming at 2 AM when he finally was able to rid his game of this corrupt CC.... @igazor
ETA: The question being, could this counter hide in a save file if it's been deleted from the dccache and dcbackup folders?