IMO, best practice is to have changes that result in a coherent revision history for the files involved.
So, rather than deleting the existing files and moving the new ones into the folders (git mv), better to copy+paste the data and delete the _later/ file. (Or just replace the file normally, so it looks like a regular revision, rather than using git mv...)
Nearby, I noticed that on US20, CRX49 has been upgraded to an interchange, and could be repositioned slightly.