After decades of Protestant expansion, this event resulted in the final conquest of the region by the Catholic Church. - clarify please.
Done
iconoclastic attacks - please clarify what you mean by this. How would iconoclastic attacks help further the Protestant cause?
Done - I've made a small modification to the text. The iconoclastic attacks on Catholic material would have reduced their imagery/paintings/whatnot. If you think otherwise, I'd be fine with putting the mentions of the iconoclastic against Catholic imagery in a separate sentence.
independent republic - isn't it a city, not a republic?
Done
After 1571, the situation changed abruptly in Besançon - this seems awkward, please reword. Also, please explain why the situation changed.
Done - I've attempted to clarify it.
In 1572, the St. Bartholomew's Day massacre caused an increase of violence in the region, and those who were expelled from the city gathered in Montbéliard and Neuchâtel before marching to Besançon in 1575. - Are you sure this is relevant? What significance did the meeting in Monthbéliard and Neuchâtel have with this conflict in Besçanon? Did they gather in 1572 or 1575 or some year in between? Suggestion: "In the midst of growing violence in the region after the St. Bartholomew's Day massacre in 1572, the Protestant personae non gratae gathered in Monthbéliard and Neuchâtel."
I think that those who were expelled from the city gathering, before launching their attack on the city, is of significance. I'm unsure when the gathering occurred, but it was certainly as a result of the St. Bartholomew's Day massacre, in which many Huguenots were assassinated by Catholics.
obtain the keys of the Battant through a man named Le Goux, after threatening notary Jean Papay - Please clarify what's the relationship between Le Goux and Jean Papay?
Done I've added a wikilink providing information about Papay's role as a civil law notary, but do not know the details of the relationship between them.
those who were approaching the Battant passed along the Rue des Granges - please clarify. Specifically: what's the Rue des Granges?
Done
Both groups were joined by many townspeople. - Did the townspeople help them? Did they try to hamper the invaders's efforts, or just observe?
Done, the former
such as Pierre Nicolas. - who is he and why should the reader care that he was hanged?
Good point. Removed.
were dragged onto a stack of bodies - do you mean thrown into mass graves? please clarify.
Done
significant financial compensation - any info on what that compensation was. It's alright if the source doesn't say.
I can't find any further information.
François de Lette - please detail the significance of this person
2a. it contains a list of all references (sources of information), presented in accordance with the layout style guideline.
2b. reliable sources are cited inline. All content that could reasonably be challenged, except for plot summaries and that which summarizes cited content elsewhere in the article, must be cited no later than the end of the paragraph (or line if the content is not in prose).