You cannot replace a shape layer with a footage layer, but if you pre-compose a shape layer, you can select the nested comp in the timeline, the new asset (footage/image or other composition), hold down the Alt/Option key, then drag from the Project panel to the Timeline to replace the layer with the new asset.
The Catch-22 is that any animation on any attribute on a shape layer will transfer with the shape layer to the new nested comp (the pre-comp). Pre-composing is the action you take to create a nested comp from selected layers.
The workaround is to create animation presets for your animated shape layers and apply them to the new assets. Pre-composing a shape layer is only a way of replacing what was originally a shape layer with an asset from the Project panel.
If your expressions are on the shape layer contents like Contents/Ellipse 1/Ellipse Path 1/Position, then the expression will have to be rewritten to take into account the Comp Space position of Ellipse 1. If your shape layer does contain multiple contents (shapes) and they are individually using their individual position or their individual transform properties, you could turn the shape layer into a guide layer and use position, or anchor point expressions like this to tie the position of an image layer to the position of an Ellipse using a fairly that offsets the Ellipse 1/Transform/Position property by half the comp with and height. This is what that would look like for Shape Layer 1 with an Ellipse 1/Ellopse Path 1/Position animation.
src=thisComp.layer("Shape Layer 1");
elps1 = src.content("Ellipse 1").content("Ellipse Path 1").position;
mstr = [thisComp.width, thisComp.height] / 2;
elps1 + mstr
This assumes that the position, scale, and rotation of the shape layer are all at the default values of comp center, 100%, and 0º. You can compensate for those changes if you like as well as any Group or object transform property.
If you show us a screenshot or give us a detailed workflow and animation description we can point you directly to a solution. I hope this at least gets you started.
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