You may check-out the work-around found here [connect.microsoft.com]

Thanks a lot for this koahnig, I clearly hadn’t come across that page before (http://www.bottledlight.com/docs/lnk4099.html [bottledlight.com] for the workaround itself).

Anyway, I applied the workaround, compared my new link.exe file against the original version to make sure that I had properly applied the workaround, and yet I still get that LNK4099 warning…?! I even renamed link.exe and tried to build my application which (obviously) failed, telling me that I indeed modified the right file, but still no luck…!?

I did not apply myself. So far, I can live with this warning even so I agree that it is a nuisance. The information seems to have already some layers of dust. It came actually before msvc 2008 and msvc 2010. I did not see this.

FWIW, I had another look at my LNK4099 warning issue and managed to get rid of it by adding /ignore:4099 as a linker option. Apparently, /ignore is an undocumented option. Whatever the case, it works for me and thought it might be of use to other people in my situation, i.e. wanting/needing to build their Qt application using MSVC.

Thanks for sharing your findings.
With google you find some references, but those are not ms pages. So, you are probably right that it is an undocumented feature.