Settings are stored in %USERPROFILE%\AppData\Roaming\PreSonus\Studio One 3\. It won't be uninstalled by the Studio One installer. So if you uninstall and reinstall Studio One, the previous settings will be used.
To solve it rename/remove the entire USERPROFILE%\AppData\Roaming\PreSonus\Studio One 3\ folder or open "%USERPROFILE%\AppData\Roaming\PreSonus\Studio One 3\x64\Vstplugins.settings" with a XML or text editor and disable (0) scanAtStartup, or remove the entire URL type attributes with the path to the VST2.x location.
<Attributes scanAtStartup="0">
<List x:id="userPaths">
<̶U̶r̶l̶ ̶t̶y̶p̶e̶=̶"̶2̶"̶ ̶u̶r̶l̶=̶"̶f̶i̶l̶e̶:̶/̶/̶/̶C̶:̶/̶P̶r̶o̶g̶r̶a̶m̶ ̶F̶i̶l̶e̶s̶"̶/̶>̶
<̶U̶r̶l̶ ̶t̶y̶p̶e̶=̶"̶2̶"̶ ̶u̶r̶l̶=̶"̶f̶i̶l̶e̶:̶/̶/̶/̶C̶:̶/̶P̶r̶o̶g̶r̶a̶m̶ ̶F̶i̶l̶e̶s̶ (x86)"̶/̶>̶
</List>
</Attributes>
Also keep in mind, Studio One does not have a bit bridge, so adding a path containing x86 (32 bit) VST's to a x64 (64 bit) version of Studio One (and vice versa) is redundant.