So, there was no answer posted on this, but here it is:
Most likely what is happening is that there is a very large file (most likely one of the generated lookups) in your ES install. Before performing an upgrade, ES makes a backup. It creates this backup using Python's zipfile module (I believe), which does not handle large zip files by default (see: https://docs.python.org/2/library/zipfile.html). When the back fails, because it gets too big, you get the error.
To solve, find the large file (again, usually a CSV), move it out of the apps directory, do the upgrade, move the file back to where you found it.
