Changes to the webapp will not migrate to the mxd. The webapp is consuming the mxd's layers.
Changes to the mxd need to republished to Portal for the webapp to see them.
Under current Portal versions, when you change and republish the mxd, it will cause certain modifications made in the webapp (like renaming layers, etc...) to be overwritten with the new mxd info. (or the layers will go back to the previous names. If I recall, the same thing applies if you move the order of the layers around.)
I believe the 10.5 release of Portal is going to address some of these issues.