Which settings? In Notepad?
If you mean in Notepad, it will go back to its default of displaying only txt files to open the next time you use it.
I'm not suggesting you change anything yet.
If you're talking about the changes suggested in http://www.gameboomers.com/Members/DOS.htm
I don't see anything there that would cause any problems with Windows. But you may not have all the files that are mentioned in that file. For example, if you don't have a Toshiba CD drive, it's unlikely that you have a Taisatap.sys file on your computer. And if you do, the path might be different to where the file is on your hard drive.
However substituting DEVICEHIGH wherever you see DEVICE in the config.sys should not hurt anything.