There are two WAD/IDX pairs in the game. One of them contains mission references, second contains binary data.
There is a tool that splits WAD/IDX pairs into single files, so those files are reworked, but the single binary files extracted from POSDEFS are not reworked.
Get the splitter for WAD/IDX pairs here:
Download Bullfrog engine IDX/WAD file pairs extractor
Or maybe you prefer already extracted files:
Download Syndicate Wars extracted IDX/WAD files
Reworked WAD/IDX pairs:
POSDEFS.IDX POSDEFS.WAD ALLTEXT.IDX ALLTEXT.WAD