What could have happen if Prussia had defeated Napoleon and his man at Jena-Auerstedt?
As already said, this would reuire an earlier POD allowing for a whole different Prussian army and leadership to fight at Jena and Auerstädt. Essentially you'd need to do the reforms that happened later to happen earlier. Given that some Southern German princes started reforms already before the French revolution and that said revolution already proved to change military doctrine and the way to govern a land and equip an army, there are plenty of lessons to be learned. However, you'd need a POD that allows for an earlier reform agenda to be enacted.
Prussia had stayed neutral the year before and remained outside the Third Coalition, in 1806 they practically engaged the French armies (who were already stationed deep inside Germany) on their own. IIRC, Prussia had about 200.000 troops, France and the CotR c. 300.000.
Stupid move by a weak king.
Jene I give to Napoleon as field commander in any case, while the parallel battle of Auerstädt might go against Davout and for the Prussians who had more than twice the numbers. But it won't be a crushing defeat of the French army.
So many factors are against a Prussian success that I cannot see the events you describe. The Prussian army was nearly obsolete in 1806 without major adaptations to modern warfare since Fred II died. The state administration and logistics were a sorry mess of sometimes feuding feudal holdovers.
You can get a Prussian success in 1806 only if you give Prussia a good reason to modernize earlier. In OTL they needed a good six years to recover and become a Great Power once again, so basically, you might need a PoD with Prussia joining the Second Coalition around 1797 and getting decisively beaten by 1799, opening the way to reforms. Of course, that will create a lot of butterflies.
EDIT: This is Prussia in 1795, pre-Basel. I believe it will lose no other territory to France in an ATL 1799 defeat than the parts of Cleve and Geldern west of the Rhine (to the left of the fortress of Wesel in the map). Perhaps East Frisia to the Batavian Republic, but even that is unlikely in 1799.
EDIT 2: This map has some errors: The area marked as "Kaiserreich Russland" is, in fact Austrian West Galicia. And the dotted border of the HRE is all wrong for any year.
People (particularly the Prussians of the day) need a real reason to change. Their attitude was 'yeah, sure the French have beaten up some Russians and some Austrians *chortle* but EVERYONE does that... now let's see how they stand up the the sheer power and overwhealming magisty of the army of Fredrick the Great!!!'
Oh, we've just had our arses handed to us. We'd better do reforms.
To do the reforms before Jena-Auerstadt require a reason.