If I got what you wish, maybe you can try this: duplicate your "multi mesh city" in a new layer.
Then join all "city copy" elements (CTRL-J) into one single object
Then in top ortho view add a plane on top of the "unified city copy", like this:
Now select the plane, then the "city", enter edit mode, then press the space bar and type "knife project", you get this
Only remember to enable "cut through" to cut through all the mesh height.
To better see what happened, after inverting selection (CTRL-I) and hiding (H) you get this:
Here is how it goes:
As you see you only get "intersecting shapes" cut, so then you should get back from the original "Multi mesh city" all buildings internal to the cut...
in my test the "cut through" is needed by my test is very simple and rough. I can't get the "knife project" to also cut away the central block, unfortunately, no matter which cutting shape used - I feel that it could be a little bug, it depends on what was the intended behaviour but perhaps it was meant to cut connected meshes, so not as in my example...
However, here is what I mean with the last paragraph: after cutting, you could separate the part of mesh selected (cut by knife project) into a new object
but as said the city part that was internal to the cut is missing... you could get that missing city part from the original multimesh city (do you remember, I said to make a copy in an other layer...)
or, you can get it from what remains from the joined city after the cut operation
to do so select what remains of the starting joined object, and in edit mode select all then use "separate by loose part",
which separates each block as its own object. So you could get the missing (center) blocks
however you get that central block select it and the cut block
and then join all
I guess you have already figured it out this, but may be useful for other readers.