The version with the earlier modification date (on the left in my screenshot) is marked as a duplicate. In my case, the newer version is a smaller version of the same font that I created for Web use, so I do not wish to delete either of them.
- Duplicate Fonts.png (11.39 KiB) Viewed 3696 times
In your case, the newer version of Arial may be after a Windows update. Do take special care when deleting windows System fonts. MainType might prevent you from doing so. I am not sure what happens in the case of duplicated System fonts. To be safe, export the font as a backup where MainType won't detect it again, then delete the marked duplicate.
Let us know your results.