We're also having this problem. Did you get it figured out?

you can change the title of the file,

but you can't change the actual file name in c5,

All the file ordering functions rely on the file name, not on the title.
It's kinda silly we can't rename files...

This would be a good idea for an addon.
One problem with file names in the concrete file manager is that the file manager will allow uploading of duplicate file names, for example a user who uploads several images from an Ipad without naming the files first will end up with the files all named 'image.jpg'.
Whilst the images will display okay on a web page, it does not help with SEO ranking.
Also, If we select "All" images from the file manager and try to download them as a zipped file, only one of the image.jpg files will be included in the zipped download..

This is pretty old but in case case you or someone who finds this post, if you'd merge the changes in this pull request you could rename files in the properties dialog:

https://github.com/concrete5/concrete5-legacy/pull/1912......

I'm not sure whether I'll actually merge this into the official version as I have a number of reasons against it, but maybe it helps someone anyway..

I haven't found a nice way to do this in a package as this dialog is part of the core and overriding a file with 500 lines in a package isn't what I'm looking for..