He probably has CUE files that reference the original WAV file(s) and not the actual compressed result.
When I drag a folder containing CUE+IMAGE into my foobar2000 playlist viewer, and then fb2k reports an error, it is EXACTLY what I want.I do not want foobar2000 to mask anything. I do not want foobar2000 to search and replace anything. I want to know about the exact state of my filesystem. In these "CUE reading error" cases, I right click and go to the containing folder and edit the CUE sheet. if ones long term goal is a perfect filesystem and perfect tags, this is not achievable if one uses "filtering programs and plugins".
so it's very much doable and probably real easy to program.
fb2k doesn't add unnecessary optional features.
that is clearly not a fb2k problem
the foobar2000 SDK is here - http://www.foobar2000.org/SDKhave fun.