Handling retraction when using a mixing extruder (2 in 1 out)
I found this post on the S3D Forums that seem to have some interesting information on custom scripting within Simplify3D. While this doesn't seem to SPECIFICALLY address the question you've got, it looks like there's a "Retraction Scripts" tab that you could probably leverage your T2 tool inside of, using "OLDTOOL" instead of "NEWTOOL". 

For additional information on what variables are available, I found a different forum post here that seems to have some documentation on Simplify3D's built-in script variables. Additionally, from the GCode in the first link's example scripts, it appears that you should be able to actually address M-commands to individual extruders (such as T2 in your case) simply by adding "T(x)" as a parameter to the individual command. I just ran a quick test on my own Marlin-based printer with a 2in-1out hotend, and I was not able to get it to address G1 commands to specific E motors without switching tools. 

All in all I think you should be able to use the custom scripts available in S3D to accomplish what you want by switching tools in the layer change script, but aside from that, I don't know what options you have available with that specific software chain.