Almost always a moved folder, a permission, or a cache that can be thrown away.
Mindex remembers the path, not the folder. If it moved, open it again from its new location — ⌘O / Ctrl+O.
External disks and network shares have to be available before the vault can be read. Mount it and try again.
On macOS, a vault in Documents, Desktop or Downloads may need permission the first time. Grant it when asked, or in System Settings under Privacy & Security → Files and Folders.
.mindex/cache.json is derived from the files and can be deleted safely:
rm .mindex/cache.json
Mindex rebuilds it on the next open. Nothing in your notes is at risk — the cache holds no content that is not already in the Markdown.
A note with malformed YAML is reported rather than stopping the vault. Open it
in raw mode and fix the block between the --- fences.
The first open of a big vault has to index every file. Later opens read the cache.