From Hydrogenaudio Knowledgebase
Oggenc2 is an enhanced version of oggenc developed by John33. Features compression from lossless files (Monkeys Audio, LPAC, FLAC, OptimFROG, WavPack and Shorten - requires presence of decoders), and the ability to specify 'padding' in the headers for subsequent insertion of Tags.
Most of the time, Oggenc may be replaced by Oggenc2, as the latter recognizes the former's switches.
If the application that uses Oggenc is hard-coded to find "oggenc.exe" (or its equivalent in *nix), you can simply rename "oggenc2.exe" to "oggenc.exe" and overwrite the original "oggenc.exe".