If you refresh windows, it will of course overwrite the old version of windows. There are some things that are not desirable about the course of action though.
1. There may still be files that will be hanging around in the background causing trouble
2. If it is a virus overwriting will do nothing for that situation and you will continue to experience difficulties
3. Sometimes a simple scanreg will help with some of the difficulties.
4. a delete windows and reinstall wil make windows think its the only thing on your computer, and thus will not see the other programs running on your computer. Doing a refresh of your os will have all the links remain in tact. As well you will not have to reinstall any chipsets or drivers.