That is the "Simulation Target".
You should try and replicate the same in the corresponding "custom code" panes under "Code Generation" settings, I think. May be you could add the location folder(s) as well/instead.
Otherwise source code for your TI target will not consider your custom code files.
There may be other ways to achive the same (e.g. customising the embedded coder target TLC file), but hopefully that should be enough.
You could check if it does the job by editing the build batch file and makefile - to see if the custom code files have been picked up.