I think one of the real plumbers will have to chime in here. But from a DIY perspective, I'd replace the copper with the flex line. If not, you need to inspect the copper to see if it can be reused or cut back first and see if it is long enough. If you keep the copper you may be able to reuse the compression nut if it will fit the new fitting. If you get a new elbow it may have the compression fittings on it. You'll have to make sure the flex line has the same size as the under sink fitting. I don't know about your inlet valve assembly, you'd need to research that some more.