Forgive me if this is already something being worked on (I seem to recall it was discussed in a recent thread) but I've used other website software where if you go to delete an image or file that is used somewhere in the project, you'll get a warning dialog alerting you to the fact that you're trying to delete an asset that is currently in use.
This would be a nice little bit of insurance (and make the program all that more appealing to those of us with flakey memories lol.)
One thing I wanted to add on this is that right now the export of only used files is flawed in that it cannot read items used within JS files. Not sure about CSS files if you have images referenced in it.
A feature for this to tell us where something is used would need to go further than the export feature does. The export feature really needs to be updated to include all files as well, and I'll will assume that if you get it working for one, it should probably help with the other.
The Export only used files feature is pretty useless as it is right now. It needs to see what's in JS/CSS files (I'm adding CSS here only because I don't know if it's reading those or not, if it is you can ignore that).
The same goes for the detection of where a file/image/etc. is being utilized. It has to be able to read within all files not just the base HTML code.
I think where this is going to be an issue is that all JS and CSS files are referenced on all pages. Maybe that's the place to start in order to get both of the above features working? Fixing so the pages only reference the JS and CSS used on that page would probably allow the above features to really see what the HTML pages are truly referencing for files/images/etc.