Yep, this is the right place. Have you tried $L delete clip? (You would need to construct a clip first, of course.) I can't tell from the documentation if it deletes the clip object from memory, or deletes the contents of the clip from the layout.
If that doesn't work and you really want to use DESIGNrev, it does accept Tcl -- you could create a script that for a selected region (clip) gets a list of objects in the region and then iterates over the list to delete each one. (I think it would be simpler to just create the clips, write those out as a layout, and XOR the two databases, but that isn't DESIGNrev.)
For adding the new IP, assuming it is in the same layers, coordinates, precision, etc., as the original, there is an example in $L create cell.