So when that happened to me I was as confused.
TL;DR: Remove ./vesktop/sessionData/Local Storage/leveldb/ directory (or rename to .old or whatever so you can try recovering its contents later)
If you use Linux and flatpak, the full path for Vesktop is:
~/.var/app/dev.vencord.Vesktop/config/vesktop/sessionData/Local Storage/leveldb/
Letting that dir regenerate immediately resolved my issue, but I had to log-in to Discord again. And discord-based settings were reset such as the theme, showing server memberlist and yeah. But Vencord settings were unaffected, and nothing was lost.