Every time I change anything on settings.json even if it's just a color, WorkSpace Anchor gets deleted and I get prompted to "Click to start scanning"
After the first scan, store the anchors in a sqlite database (or whatever vscode extensions can use as storage) then compare the changes every settings.json update.
The only change that warrants a re-scan would be adding a new custom anchor tag, I believe. if you delete or disable a tag you can just hide or remove the old rows.