With Forward Error Correction, what bit rate should be used in a link budget?
Coding gain provides an indication of the improvement in performance when you use a particular code, and for this to be meaningful the error rate curves for the encoded case are plotted against Eb/N0 where Eb is the energy per information bit actually transmitted.  Here's one reference on the web:
http://ecee.colorado.edu/~mathys/ecen5682/slides/convperf99.pdf

so no, you don't modify Eb to allow for the fact that the redundancy of the code has increased the transmitted bit rate.