Hello.

It is an often scenario that users modifying default web part in order to get some additional functionality. It does not mean that you can´t do an upgrade in the future.
However, when modified some default files (any file in default solution), you should always make sure that these files are not override when doing upgrade, or applying hotfix.
This always depends on particular upgrade / hotfix package, whether it contains new version of given files, or not. So, you should always check content of given upgrade / hotfix package to see, whether it contains new version of file(s) you modified before. If so, you can simply choose to not copy them. Also, you should always backup your files before do any upgrade / hotfix, so you can reverse changes if necessary.

Best Regards,
Radek Macalik