Deleting the whole VirtualInstall folder isn't neccessary. I found that Vortex continued to think I had mods enabled until I went to my VirtualInstall folder and edited the VirtualModConfig.xml file. In the VirtualModConfig.xml file there was an old mod that must be from a previous installation. I deleted this node from the <modList> so that the file showed like this:
<?xml version="1.0" encoding="utf-8"?>
<virtualModActivator fileVersion="0.3.0.0">
<modList></modList>
</virtualModActivator>
Vortex then was able to continue successfully with the mod import process.
