A great analogy for this would be along the lines of don’t put your hands in the hive if you don’t want to get stung!
In other words, be extremely careful in modifying the built-in SharePoint files.
“From the MSDN site Link (emphasis added)
Except for a few well-defined files such as the web.config or docicon.xml files, you should never modify the built-in files included with SharePoint Products and Technologies except through official supported software updates, service packs, or product upgrades.
This type of customization is not supported.
Modifying the files that are installed by SharePoint is not supported. However, there are some scenarios in which you may have to modify these files to achieve consistent branding or other customizations. When you modify these files, you must consider that they may be replaced by future updates and service packs. Additionally, there may be complications when you upgrade to later versions of the product. Keep backup copies of all customized files in case they are overwritten by an update. Product support will provide commercially reasonable support for help with modifications but will be unable to provide product changes or hotfixes that result from modifying the files that are installed by SharePoint.
- Modifying Built-In SharePoint Files (From MSDN)
- How to customize application pages in the Layouts folder in SharePoint Server 2007 and in Windows SharePoint Services 3.0.
- GOOD – documentation has been provided as ample warning
- NOT SO GOOD – would be nice to have a really simple method of customizing, rolling back and not having to worry about hotfix, service pack, upgrade possibly breaking the changes.