In the Calibre folder setting >
gui.json file > "library_usage_stats" proprety
Code:
...
"library_usage_stats": {
"E:/Calibre/Comics": 212,
"E:/Calibre/e-Book": 5940,
"E:/Calibre/edition": 216
},
...
Delete the unwanted line/library. Be careful, the last line ("edition" in this case) don't have comma at the end.
(copy and save a bakup before any operation)