If I am understanding you correctly, this is what I do.

Leave the percentages alone.  As Lisa alluded to, at some point you will need put stuff back in.  Who can remember what that will be X number of years from now?  Since this is depreciable real property, I take the undepreciated basis and put it/add it to land.  I make a sub-schedule indicating the amount and date it was done.  That will stop all depreciation.  If it is ever placed back into service, I know what I have to remove and whatever other modifications I will need to do at that time to make things calculate correctly again.