Support Scenario where S3 Path is a File and used to correspond to a Directory and still has version of key there

Originally formulated in

- https://github.com/dandi/s3invsync/issues/170#issuecomment-2691822753

It seems we encountered "design" issue with our solution: it could indeed be legit that we have some old versions (thus would be with versionId's in the suffixes) for keys under `key/` subfolder, while the most recent version present in the `key` file thus forbidding for the `key/` to exist at all! e.g. smth like

```shell
mkdir -p key; echo content > key/subkey
# snapshot to S3, update inventory
rm -rf key
echo content > key
# snapshot to S3, update inventory
```