I am unsure if it helps and if I understood, so here is what I do:
- open project
- change option(s), including your problematic one
- save project
- build project [SHIFT-F9] (not compile)
- test project (run)
I assume you do just run/F9/compile to test, that way the resources are not recompiled all-the-time correct so it uses an old one where the changes arent updated yet.