Well, it's not a problem unless you do a lot of customization to the core files. Those updates will overwrite those custom files and your work is lost.
To avoid this, you need to detect and merge the differences of each file, compare source code, compare program output, etc.
Below are a few software that can do the job of comparing files side by side indicating which lines of codes have been changed or any code that you have customized vs the upgrade files.
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