Can I replace apps from root/system/app folder before installation?

Hi guys, I am using @fa1zali Optimus ROM v4.4.2, I got some issues so I am thinking of installing the same ROM again. I don't know much about android development but, if I extract the ROM package and replace the old apps from "root/system/app", replace them with the new ones(renaming the new ones with same name) and zip it again. Is it going to work or not? because if they are logged in some file then its not going to work.
And if I add some more apps there, they will get installed or not?
I am thinking of updating all apps before installation if its possible.
Thanks