Try the following (in order of pain magnitude):
1) Project > Synchronize Modification Dates.
2) a. Write down all of your project settings.
b. Quit CodeWarrior.
c. In your project folder, delete the folder yourProjectName_Data, where yourProjectName is the
name of your CodeWarrior project.
d. Restart CodeWarrior, and hopefully all will be well.
This option cleans out a lot of state information that the IDE relies on. This state info might have gotten corrupted and is source of your problem. The downside is that you might lose some of your project's settings, which is why you write them down.
3) If you are using source control, it might be touching the files so that they all appear to have been revised. I do not know of any workaround for this.
---Tom