The main game I'm working on has a lot of sentences ending in ~, so I got curious and decided to run them through Sugoi and see if there was any difference. My sample size was pretty small (like, 20 instead of hundred), but I had some additional context since I know the tone of the game/characters.
For the most part, there wasn't any noteworthy difference. The majority of lines ending ~ were small things like "Beautiful~" so there isn't much room for context to really matter. Here's a small selection of lines which were different based on whether I included the ~ or not:
Based on what I saw and memories of ~ use in manga, I think escaping and re-adding the ~ would be best for both avoiding errors
and translation clarity.