FileBot

I run the portable version of Filebot. and I upgraded to newest currant version thus deleting the previous and I had to re register the application
I assume this is just an issue when updating the portable version it wont cause me to get flagged for abuse or anything

Not a problem. If you use the portable version, then the user data folder will be in that folder too. So if you grab the latest portable, you'll also want to copy over the user data folder from the previous portable, as to import all your user data including license information.