The Holy Roman Empire was larger than you might think, even in 1789, and included lands in France and Italy that might possibly never have had any Protestant clergy.
There were many ecclesiastical states ruled by Roman Catholic clergy remaining in the Holy Roman Empire in 1789. Most of the prelates who ruled those states would have been strongly opposed to Protestantism, though there were examples of prelates who didn't oppose it. Any ecclesiastical state which had an unbroken succession of anti Protestant rulers from three centuries since the Reformation might possibly never have had a single Protestant pastor in a single parish. The ecclesiastical states seem like a good place to look for parishes without Protestant pastors for 300 years.
In 962 Otto I the Great, the mighty King of the East Franks or Germany and of Italy or Lombardy, was crowned Emperor in Rome. From 962 the positions of King of Germany and King of Italy were attached to the position of Emperor. In 1032 Emperor Conrad II acquired the Kingdom of Arles or Burgundy and from 1032 the position of King of Arles or Burgundy was attached to the position of Emperor.
The Kingdom of Arles or Burgundy included western Switzerland and the southeastern sixth of Modern France. The Kings of France gradually acquired various fiefs in the Kingdom of Burgundy over the centuries. And it is common for historical maps to show such fiefs as being in the Kingdom of France and no longer in the Holy Roman Empire after being acquired by the King of France. But is it accurate?
I note that the title of the King of France in the Kingdom of France was King of France and of Navarre. Here is an example from 1690 in the Reign of Louis XIV:
(Jan 1690) [5: tome 23 (1883); p.503]
< Louis XIV (+1715), King of France 1643 >
Louis, par la grace de Dieu roy de France et de Navarre
But in Provence and Forcalquier in the Kingdom of burgundy in the Holy Roman Empire the title of the King of France was King of France and of Navarre, Count of Provence, Forcalquier and adjacent Lands. Here is an example from 1789:
(Mar 1789) [3: p.164; Doc.# LXXXIII]
< Louis (+1793), King of France (Louis XVI) [1774-1792]; Count of Provence [1774-1789] >
Louis, par la grace de Dieu, roy de France et de Navarre,
comte de Provence, Forcalquier et terres adjacentes
In Dauphine the title was King of France and of Navarre, Dolphin of Viennoise, Count of Valentinois, Diois. Example from 1789:
(July 1789) [55: p.9]
< Louis (+1793), Dolphin of Viennois; King of France (Louis XVI) [1774-1792] >
Louis par la grâce de Dieu Roi de France et de Navarre,
Dauphin de Viennois,
Comte de Valentinois et Diois
So it seems to me that a lot more of the Kingdom of Burgundy remained in the Holy Roman Empire than most historical maps show.
In Italy, lands that remained part of the Holy Roman Empire until the French Revolution included Piedmont, Genoa, Modena, Montferrat, Mantua, Parma, the Grand Duchy of Tuscany, etc.
Ecclesiastical states which lasted until the French Revolution included The Archbishoprics of Salzburg, Trier, Mainz, & Cologne; the Bishoprics of Augsburg, Bamburg, Brixin, Constance, Eichstatt, Friesing, Hildesheim, Liege, Paderborn, Passau, Regensburg, Speyer, Strasborug, Trent, Worms, and Wurzburg; plus 23 imperial abbeys in the Bench of Swabian Prelates and 19 imperial abbeys in the Bench of Rhenish Prelates.
Since most of the prelates who ruled those states would have fought strongly against the reformation (though there ae examples of prelates who didn't), a state where each and every clerical ruler for 300 s years was strongly opposed to the Reformation might not have ever had a single Protestant pastor in any parish. Thus the individual history of each of those states, and especially whether all of the rulers strongly opposed the Reformation, would be a strong clue to which of them would most likely have had parishes that never had Protestant pastors.