You can ask on the mailing list, or get involved in the Flex project yourself. I think the code-base for GNU Flex has remained static for a while, but I don't know who maintains the Windows port. In the interim...
I would recommend including the produced source in your project.
- Generate the lexer on a Linux system to produce your lex.c/lex.h files (or whatever)
- Include those files in your Win32 C source before you build
If you don't have direct access to a Linux system, a virtual machine might be a good idea. The Flex source should be complaint to some C standard that builds on Windows, but most of the POSIX differences can be altered to use Win32 API fairly easily.
Maybe distribute as:
/src/source_files.c
/src/lex.l
/src/win32_lex/lex.c
This way systems with a modern flex can generate the source from the lex file, and Windows systems compiling the source can use the complementary pre-processed C files.
Short of using some user-space POSIX (Cygwin or whatever).
A little bit of tweaking required, but isn't that portability for you!