If they are identical, then why did you need to change the names? BTW, changing them in pathfinder doesn't change the part file it will continue to point to.
You would need to right mouse click on each part [other than the first one] and choose from the "More" drop down menu, "Replace Part with Copy".
Then save each with a unique name....then you can create your cutout[s] either as an assembly-driven part feature[s], or as part feature[s]. You could even go into each part to make local edits to that part on it's own.
There are several ways to do many things in Solid Edge, but it does depend on the actual edit [cutout] you want to apply, as to how a particular process might be used.
Sean Cresswell Design Manager Streetscape Ltd Solid Edge ST10 [MP6] Classic [x2 seats] Windows 10 - Quadro P2000