Complex sentence: Nevertheless, it is important to understand that one of the aggrieved parties will not see it that way, as the edit war has been effectively resolved for the period of protection in favour of the last edit, regardless of your intention.
Split into simpler sentences: Nevertheless, it is important to understand that one of the aggrieved parties will not see it that way. By protecting the page, the edit war has been effectively resolved in favor of the side that had the last edit for the length of time that the page is protected, whether or not that was your intention.