[Bug]: Big folders randomly stop syncing "because they are too big"

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- [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

Every now and then, Nextcloud randomly deselects a lot of folders, showing a message they were not synced "because they are too big". However, these folders were previously synchronizing just fine, and I have only configured Nextcloud to skip *new* folders above a certain size:

(so I do not have the disable when folders grow above the limit enabled, which #6097 suggests causes a similar issue - or maybe it is actually the same issue caused by the size limit for new folders)

When this happens, my Nextcloud settings view looks something like this:

This has been happening every now and then for quite some time (months, maybe two years?). In the past, I could usually fix it by pausing then sync and then restarting it, which would then show all folders as checked again. This time, it seems that pausing and resuming does not work, so I finally took some time to file a bug report for this.

Once, I tried to fix it manually by rechecking boxes, but that ended up re-uploading files that were deleted on the server in the meanwhile, which is not quite what I want. This is also why I am very hesitant to click any of the buttons in the settings window - no clue what will happen exactly.

Recovering from this situation is complicated because in some of the synced folders I had some big subfolders unchecked to not sync them (but I am pretty sure this does not apply to all folders - it seems basically Nextcloud just unchecked *all* folders > 500MB.

### Steps to reproduce

Unclear. This seems to happen randomly and I have not been able to figure out a clear cause yet.

### Expected behavior

When I configure folders to be synced, they should stay syncing as configured and not turn off randomly.

### Which files are affected by this bug

-

### Operating system

Linux

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

Ubuntu 25.04

### Package

Official PPA

### Nextcloud Server version

31.0.4

### Nextcloud Desktop Client version

4.0.4

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

Updated to a major version (ex. 3.16.3 to 3.17.0)

### 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

_No response_