When an annotation processor is working with a file - say, a resource found in the source location - and calls FileObject.toUri on it, normally (assuming #6419926 is fixed) a file:/... URI is returned which can then be used to refer to that resource, say by passing it to an XML parser.
When however the source tree is located on a Windows UNC share (\\server\share\path\...), the returned URI is of the form
file:////server/share/path/...
This has well-known problems documented in #4723726; namely, the normalized form is
file:/server/share/path/...
which translates to a different (likely nonexistent) file path.
The desired form is that specified by Microsoft:
file://server/share/path/...
(Of course other code such as XML parsers then needs to handle proper UNC URIs as well, but that is outside the scope of the compiler.)