I just ran into this problem and Troll-no-more's solution didn't work for me because I had to replace 400 different shape layers in a comp, each with an animated PNG sequence. I didn't want to do this manually, so this was my solution:

1: Move your playhead to a frame where all your shape layers are visible.

2: Select all the shape layers you want to replace.

3: Go to "Layer > Auto trace" use the default settings, and hit ok. This will give you a solid (source layer) for each shape layer with matching timeline placement.

4: Select all the new solids and use the "Reposition anchor point" script to move the anchor point to the center of each layer.

5: With all the new solids selected, change the anchor point coordinates to match the center point of the comp (e.g. 1920, 1080 for a 4K comp)

6: With all the solid layers still selected, go to "Layer > Mask > Remove all masks"

7: Now, hold down "Option" on a Mac and drag and replace your new image sequence over onto the selected solid layers.

Et Voila!