If all these are changed and replaced, what is left is an empty shell. Then why not keep it as it is for a few more years and wait for 055, or use two 052C/D in place of one Sov?
The Sovs cost a lot of money to run, and takes up a lot of crew. It makes no sense to leave them as is while they get more and more obsolete while tying up all those resources and personnel for decades to come.
If they also change the engines, then I would expect a great deal of internal changes to improve automation and reduce the crew size. Depending on how comprehensive they want to make the upgrade, they could probably also upgrade the crew quarters and onboard facilities to bring those in line with modern PLAN standards.
All of those changes would be useful to help make the type more 'deployable', especially on long range long duration missions.
I also have a feeling that the YJ12 might be too big for even the strike length new CCL VLS. In which case, upgrading the Sovs would be the cheapest, quickest and most effective way to get those new beasties deployed on surface ships without having to design a new class of ship specifically around the beastly missile.