When receiving error diagnostics from the compiler:

Diagnostic<? extends JavaFileObject> d;
URI u = d.getSource().toUri();
File f = new File(u);

does not work. You need to use e.g.

File f = new File(u.toString());

since the "URI" is just a pathname, not a real 'file'-protocol URI.

In j2se/src/share/classes/com/sun/tools/javac/util/DefaultFileManager.java, it can be seen that the impl of RegularFileObject.toUri() [BTW why the inconsistent capitalization vs. File.toURI?] is incorrect:

        public URI toUri() {
            try {
                return new URI(f.getPath());
            } catch (URISyntaxException ex) {
                return f.toURI();
            }
        }

which should read simply:

        public URI toUri() {
            return f.toURI();
        }

Similarly, ZipFileObject gets it wrong too:

        public URI toUri() {
            String zipName = new File(getZipName()).toURI().getPath();
            String entryName = getZipEntryName();
            return URI.create("jar:" + zipName + "!" + entryName);
        }

should read:

        public URI toUri() {
            String zipName = new File(getZipName()).toURI().toString();
            String entryName = getZipEntryName();
            return URI.create("jar:" + zipName + "!" + entryName);
        }

(Not sure whether URI.toString() is appropriate here or whether e.g. URI.toASCIIString() should be used.)