There are a few things you can do. The easiest is just rename (or remove when you don't need to keep settings) the Studio One 3 user settings folder when Studio One is closed (%USERPROFILE%\AppData\Roaming\PreSonus\Studio One 3).
Alternatively when you are sure an audio engine setting is causing the issue, you can rename/remove only the AudioEngine.settings file (when Studio One is closed). It can be found in %USERPROFILE%\AppData\Roaming\PreSonus\Studio One 3\x64\.
Another alternative is temporarily disabling the audio service that is causing the issue so you can alter your change. When Studio One is closed this can be done by editing the %USERPROFILE%\AppData\Roaming\PreSonus\Studio One 3\x64\Services.settings file with a text editor.
For ASIO set the enabled status of the ASIO Driver Support to 0:
<Section path="{75E7B889-FD67-40FE-A64A-FD8269E32DFB}">
<Attributes friendlyName="ASIO Driver Support" enabled="0"/>
</Section>
For Windows Audio set the enabled status of the Windows Audio Support to 0:
<Section path="{87999874-00BD-4BD5-AAD3-F30ACA42BF53}">
<Attributes friendlyName="Windows Audio Support" enabled="0"/>
</Section>