[Bug]: Upgrading to 3.16.3 does not work with configuration from 3.16.2 (downgrade works again)

### ⚠️ Before submitting, please verify the following: ⚠️

- [x] This is a **bug**, not a question or a configuration issue.
- [x] This issue is **not** already reported on Github (I've searched it).
- [x] Nextcloud Server and Desktop Client are **up to date**. See [Server Maintenance and Release Schedule](https://github.com/nextcloud/server/wiki/Maintenance-and-Release-Schedule) and [Desktop Releases](https://nextcloud.com/install/#install-clients) for supported versions.
- [x] I agree to follow Nextcloud's [Code of Conduct](https://nextcloud.com/contribute/code-of-conduct/)

### Bug description

After auto-upgrade from 3.16.2 to 3.16.3, the configuration was no longer applied and the setup dialog was shown.
Downgrading to 3.16.2 used the configuration again.

I start with a command-line specified `--confdir` parameter. I see from the last-modified timestamps in the directory that it is being picked up, it just does not apply the configuration.
My Nextcloud Desktop client is started via:
```
"C:\Program Files (x86)\Nextcloud\nextcloud.exe" --confdir Y:\AppData\Local\nextCloud
```

### Steps to reproduce

1. Restart 3.16.2 as it asked to auto-update to 3.16.3.
2. Restart PC
3. Restart Nextcloud as usual. Setup dialog is shown like no configuration was applied.
4. Downgrading to 3.16.2 works, configuration is picked up again.

### Expected behavior

The configuration and existing sync folders from 3.16.2 should be picked up and configuration should be read.

### Which files are affected by this bug

Does not apply

### Operating system

Windows

### Which version of the operating system you are running.

Windows 11

### Package

Official Windows MSI

### Nextcloud Server version

30.0.8

### Nextcloud Desktop Client version

3.16.3

### Is this bug present after an update or on a fresh install?

Updated from a minor version (ex. 3.4.2 to 3.4.4)

### Are you using the Nextcloud Server Encryption module?

Encryption is Disabled

### Are you using an external user-backend?

- [x] Default internal user-backend
- [ ] LDAP/ Active Directory
- [ ] SSO - SAML
- [ ] Other

### Nextcloud Server logs

```shell

```

### Additional info

[20250416_2305_nextcloud.log.0.gz](https://github.com/user-attachments/files/19785031/20250416_2305_nextcloud.log.0.gz)
[20250416_2305_permanent_delete.log.0.gz](https://github.com/user-attachments/files/19785032/20250416_2305_permanent_delete.log.0.gz)