The main issue is going to be the increasing complexity. As patches and repairs get layered over each other, as buildings get moved, gradually it becomes harder and harder to understand the full system.
Once something has been patched and remade over the course of thousands and thousands of years you start getting things creep in that are not part of the original design but which are passed on down to the next generation. Things that might not be needed, or might actually make the system work less well.
These problems can be fixed by ripping out the system and rebuilding it from scratch, but if no-one really understands it or if it is tightly intertwined with thousands of other systems then that becomes harder and harder to do.