OK, so the developers finally got back to me. Here is their response.
"This error simply suggests that something has changed since minify was initially configured. Specifically, that the file in question no longer exists.
Future releases will improve the handling of this but for all practical purposes, this is merely a cosmetic annoyance and can be ignored. If you don't want to see it, select "Disabled" from the Minify error notification dropdown menu."
So, we can ignore these errors. The W3TC guys could have saved themselves a lot of bad-will by simply posting that answeer here themselves 2 months ago.