#Nexus (Beta) uninstall removed all mods including those not managed by the program

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worldly epoch
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I updated Vortex and I got an internal error that advised me to uninstall and reinstall it. I went ahead and did that but upon uninstalling and reinstalling all my mods were removed. I only had 8 installed via Vortex but it removed all of them even the one I had been working on myself and I lost over 12 hours of work with no way to get it back. Is there any explaination on how this happened? I lost over 100 total mods.