Any suggestions for software release tracking that can be updated after release?

[Nick]

Hey folks! My company's got a bit of a unique challenge. We develop software for a niche part of the entertainment industry. Our clients usually have a fair amount of input over what we make for them and we need to release different software versions with different features to each client.

This becomes pretty difficult to track who has what and who wants what. We often deploy to testbed servers before we go live on their sites, and at times while testing, some of the clients can and do object or request changes to specific things, which slows down release timetables and ends up with extremely divergent software that's modified on the fly.

What my company needs is a software versioning release system that allows us to go back after 'release' and make changes and note why those changes were made, and then have the ability to archive the entire thing once the next big release is rolled out to start again. 

I'm aware the way it's done is definitely not best practice, but it is the way it is and we're not a big enough company to tell our customers 'this is the release, take it or leave it'. Things like Kanban would be completely chaotic and don't give us the option to place them under an umbrella of a version, and most software versioning systems say once a release is assigned as being released, that's it we can't really add or take things out of it. So we sort of need something half way in between both.

Any suggestions?