Again, it depends on whether you're talking about Pycharm or Python. Upgrading one does not effect the other. Python doesn't care at all about Pycharm, however, Pycharm
does need to know where Python is, so if you upgrade Python, you may need to notify Pycharm where the new interpreter (folder) is.
As for Python, suppose you want to go from version 3.6.2 to 3.6.3 and your current Python directory is "C:\Python36", when you run the new installer, make sure the directory location is the same, "C:\Python36", this will upgrade the current version to the newer version, as well as keeping all your 3rd party libraries (which are lost if you do an uninstall/install). I would also recommend, after an upgrade, that you run
pip list --outdated
from the command line (which you should be doing periodically anyway). I do not know about Linux or Mac, as I've not had to upgrade them and to be honest, when it comes to their pre-installed versions, I wouldn't want to try for fear of 'breaking' the OS.
I will say, and this is my own personal method, is if there is a change in major versions of Python, say from 3.6 to 3.7, I will remove the older version and run the new version as a new install. I have no scientific reason for doing so, I just like to do it.
If it ain't broke, I just haven't gotten to it yet.
OS: Windows 10, openSuse 42.3, freeBSD 11, Raspian "Stretch"
Python 3.6.5, IDE: PyCharm 2018 Community Edition