Can I change the clips in a project file?

Yes! To replace clips in After Effects:

Import your own footage or images into the Project panel.
Find the original clip in the Project panel.
Hold Alt (Windows) or Option (Mac) and drag your replacement footage onto the original layer in the timeline.
Adjust the scale, position, and timing if necessary.

This replaces the original footage while preserving the layer's existing effects and animations in most cases.