Hope the undo and redo history will be retained even if you have saved a project file.

Undo history isn't lost when saving a file, either by the auto save feature running or by you manually saving the project. At least not normally.

It is deleted (as @David.Arbor ) mentioned when you close the project.

Since undo/redo is saved in RAM you may have an issue with the aount of RAM allocated to AE.

If you need previous versions, open After Effects Preferences (Alt/Option + Ctrl/Cmnd + ;), go to the Auto-Save menu and set up the timing and number of versions. These are my standard settings:

If the projects get complex, I increase the number of versions. 

Also, every time you send a Composition to the Media Encoder, you get a copy of the project file by default. This is the project folder for one of my clients for a job started on March 3 of this year:

I do the same thing for all of my projects. Everything is archived, from Illustrator artwork and proposals to my Premiere Pro and DaVinci projects. 

Hi there @jeffvalerio ,

The History/Undo stack is saved into RAM, which means, as you note, it will be lost when you close AE, just like it is in Photoshop and most other apps. The After Effects project file isn't a database (unlike a Lightroom catalog or the Character Animator project file), which means these changes can't be preserved.

I recommend you work in versions to preserve varations rather than rely on the undo stack, as you will have much more flexibilty and control over your compositions.

Thanks,
- David, After Effects Engineering Team