The famous and extensively used Object Repository (aka OR) has a major series of bugs (already demonstrated in this blog). This feature has a huge play in QTP utilization, and is a crucial feature in this tool. Can't believe it's so buggy.
Inside the OR window, there's a dropdown list where you can select which action you want to edit the containing objects. Turns out that, if you change to another that is different from the current one on QTP window, the OR (or QTP itself - who knows?) doesn't save the changes you make.
After following the steps above, all changes you made are not saved.
Workaround: Well, there nothing much to do about it, except to close the OR window, switch to the correct action in QTP and re-open the OR window. By doing so, you guarantee that the objects/checkpoint/etc you edit will be correctly updated and saved.