It depends from the way how did you make your modifications. The upgrade process may replace all modules from the package, but before start Una will inform that some files were changed and stop the upgrade.
Hello, that's why I try to touch as little as possible to the code, many things are modifiable via the mixes and the modifications made in these will remain.
Also it is interesting to follow the evolution of tickets on Gythub, then you have a good way to see what will be changed or not.
Personally, for a big update, I test it before by cloning the whole site in a subdirectory of the real site, at first it is more careful and it also allows to see which parts are affected and if modifications have have been crushed, I see it, I prepare the new files in advance, so that I have only to replace them in the actual update of the site.
So when I do the actual update on the production site, I'm just repeating what I've already done taking notes, and I'm so much more relaxed and everything is done quickly.