For workplaces to be flexible and to stay that way, generally a lot of things have to be in place.
1. The boss has to be on board.
2. It has to be implemented at all levels (ie. not just a perk for upper level management).
3. All levels of staff have to be invested in implementing it. It can't just be the CEO's brainchild. Everyone has to be in on it.
4. Everyone has to see the benefits of it. This means numbers proving the program is good for people and good for the bottom line.
5. It has to be well-managed.
Even so, as Marissa Mayer or Hubert Joly of Best Buy could tell you, even the most popular, culturally-entrenched program can be unilaterally shot down from above. There is plenty you can do if this happens to you, but unfortunately, some people can't be persuaded.
Renegotiating a flexible schedule is a little different than whatever negotiation you may have gone through to get the schedule in the first place. If your boss is determined, you may want to try to become the exception rather than changing the rule.
However, I think that in many cases, business people simply become entrenched in the typical way of doing business, and they may not be aware of all of the benefits of flexibility.
It can be extremely frustrating to have your ideal schedule taken from you, especially when you've worked so hard to get it. But though you might have to face the possibility that you might no longer get things the way you want them (and decide what you're going to do about it if things do change), no one is a better representative for what you need and want from your work life than you are. So don't give up without a fight!