Overriding encrypted IP files - specifically PLLs

If the original PLL is a standalone file, you could either remove/rename it, or modify the .qip to no longer point to it. Then just add your file. If the PLL is part an HDL file that has other things in it which must be read in, I can't think of a way. There's no way to read in an HDL entity/module and then discard it or replace it. (Configuration statements allow binding of modules to specific instantiations, but I don't know if they can be done separately.)