Yes. If you omit the full path and only give a relative path name, you can then specifying the include path in ADE - which can be relative to the working directory.
So for example, say you have an s-parameter file, file.s2p, in a subdirectory "models" under your working directory. Specify the file on the nport as "file.s2p" and then in ADE under Setup->Simulation Files, specify Include Path as "./models".
In reply to Andrew Beckett:
Many thanks Andrew