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Nice catch, +1 from me on this.

Indeed, preupg should not alter your system in any way; its job is solely to scan your system and create an "upgrade package": report plus some files.  You can run the scan as many times as you wish.

Resolved by upstream commit https://github.com/upgrades-migrations/preupgrade-assistant/commit/f914a61304bbb87e64ad3605eb7d83ea72ba1a90

preupgrade-assistant-2.3.3-1.el6:

    # preupg 
    The Preupgrade Assistant is a diagnostics tool 
    and does not perform the actual upgrade.
    Do you want to continue? [Y/n]
    y
    Gathering logs used by the Preupgrade Assistant:
    All installed packages                                 : 01/10 ...finished (time 00:00s)
    All changed files                                      : 02/10 ...running
    [...]

The message still appears at the bottom of the report, but at least does not look like it has anything to do with the y/n confirmation.

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://rhn.redhat.com/errata/RHBA-2017-0819.html