If I need to change a file (say for users that are on a subscription) for the new copy of my software. do I have to pay and update all those users again? or can I change the file in place per se?
No, it will be considered a totally new file with a new URL to download. You can set the price at $0.00 and email your subscribers the new download URL. But you will have to pay for the first upload (and every download, I think)
Files Forever is really not very well suited for software distribution. I'd recommend against using it for this.