Depends on where the presets are stored. If they're stored in the pref file, and you choose to replace the prefs, then yes... your presets would get wiped out.
You could save / move / archive your prefs file before you reinstall (or look for a presets folder) and then re-write it after you did your reinstall.
You didn't say Mac or Windows, so I can't help you on where those might be.