We are using the SoilFluxPro program from Licor, but this point and click solution is slow and prone to mistakes. We could develop our own scripts but would be happy to save the time. Chances are it has been done by several groups already. We are aware of the R flux package, but we look for something that deals specifically with the format of the 8100 files, which mixes meta data in the files.
Cheers and thanks