Just to add some information about that message specifically -
Think about this sequence:
You change some file in custom, and it overrides something in core
SuiteCRM core gets a new version of that file, and it matches changes in other files - all files need to be the new version at the same time
You install that upgrade
Problem 1: your custom file is still overriding the core file. Having a new core file is not taking any effect.
Problem 2: since the other files were changed, now there is an inconsistency in your system
So, while normally these changes aren’t very relevant, occasionally they can break your system. You should look at all those files listed in the upgrade screen, one by one, and if necessary merge your changes with the new code.
Sorry, I know this is very laborious, but there really is no way around it - the upgrader can’t guess what you have in your code…