What about instead of breaking up the Empire, have Napoleon, elected as the Holy Roman Emperor?
He could then set about promoting new "Princes" to take on the position of Elector of Brandenburg?
Removing the House of Hohenzollern from power.
Denying Napoleon the option to do that was the reason for Franz II. to dissolve the HRE.
Removing a sitting Emperor would have been rather difficult, but assuming that Franz II. dies sometime after 1803:
The electors of Bavaria, Württemberg, Baden, Regensburg were in the first wave of Rheinbund members and would have voted for Napoleon, presumably.
Bohemia, Salzburg, Saxony and Hanover would probably not, Hessen and Brandenburg are iffy, but highly unlikely: Prussia could live with the established emeperoship of the Habsburg, but granting it to imperious and dominating Napoleon would have been a capitulation. Kassel was not exactly dependent on Prussia, but a close ally.
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Concerning the thread this is in: Even for Napoleon, it would be inconsistent first to negotiate the secession of the Rheinbund states from the HRE in July of 1806 and the to recreate it in August of 1806 after Franz II. abdicates. There is no way Franz would simply transfer the HRE title to Napoleon.
But maybe it could be spun as strong resolution of no confidence against Franz II. The Rheinbund princes could be browbeaten into accepting this swerve if Nepoleon promised no interventon in their internal government and threw them some goodies. Würzburg as successor for Salzburg could be made to join, obviously, and Berg would be made another electorate, probably.
Friedrich Wilhelm III of Prussia would never agree to join a reconstituted NRE. In 1806, they were busy to create their own Northern German Empire with Saxony and Hesse as main allies.
Napoleon would have to beat Prussia up until it has no choice but to place itself under his imperial authority which he then uses to depose its ruler who has not even had the rudimentary intelligence to combine the acceptance of membership in the NRE with a "no deposal" clause?
And if Prussia is so broken that they have to accept anything without conditions (and without allies) - what does the HRE fistion help Napoleon?
That does not add up.