Juste an update on this issue for anyone it could help.
The issue came from the INCPATH section of the makefile. Though similar beetween makefile.debug and makefile.release it seems that the compiler (or linker) could not interpret relative path ('../../../') when in release mode (whereas it works ok in debug). I could not find a solution to directly fix this issue so I now modify the makefile once created/updated in order to replace occurences of relative paths by absolute path. This is done using a batch file that I execute after the qmake.exe step (step added in the compilation steps of the project configuration)