In short, Yes, but to varying levels of difficulty.
M-Files are version agnostic, though some commands may be deprecated in the newer releases.
In order to use Simulink files, you will need to be mindful of which version you are using. You can always open an older file in a newer release (i.e. R2016b will open a R2012b Simulink model), but not the other way around (i.e. R2012b will not open a R2016b Simulink model). To be backwards compatible, you will need to make sure you "export" any work done in R2016b to R2012b by going to File >> Export As >> Previous Version.