OneDrive message "Delete these items" after syncing my Desktop with OneDrive.

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OneDrive message "Delete these items" after syncing my Desktop with OneDrive.

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With a new notebook computer, initially I didn't backup the Desktop and Documents folder on that device, but then following ChatGPT decided to do so. There were three folders in my local Documents folder which I moved to another location (Classin, WeChat and QQ).
After it was successfully completed I keep getting this message when I power my device on.
I have been clicking "Keep these files".
What could be causing it, and what can I do to follow best practise?

Thanks.

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2 answers

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Answer 1

EmilyS726 264.6K Independent Advisor

That message is OneDrive’s “large number of deletes” protection. It appears when OneDrive detects that many previously synced files have disappeared from a synced folder and wants to confirm whether those deletions should also be applied to OneDrive.

You said "There were three folders in my local Documents folder which I moved to another location (Classin, WeChat and QQ)."

Can you tell me - where did you move them to? By the way, when you turned on backing up your Documents folder, this Documents folder is no longer a "local" folder. It syncs via OneDrive to cloud and all devices. So when you move anything in that folder, it will move from cloud and will sync across all devices. I think this is what set off the mass deletion. So it is important for me to know where you moved them to.

SHV 160 Reputation points

2026-09-09T00:13:54.94+00:00

Hi Emily,

I moved three folders (on AI advice) to:

I note your point about my Documents folder no longer being a local folder.

Should I move those folders back to Documents? As a matter of fact, I can see folders with those same name in my now synced Documents folder... Perhaps they are created automatically when I use those applications...

Thanks for the advice so far.
EmilyS726 264.6K Reputation points Independent Advisor

2026-09-09T00:21:37.78+00:00

Ok, so yes, those will be recreated when you use the apps.

Since you moved to a local folder not nested in OneDrive folder, the way OneDrive sees it is, you are removing these three folders out of OneDrive, hence all of the deletions. Any time you move things out of OneDrive or its sub folder, you will see deletion behavior like this.
SHV 160 Reputation points

2026-09-09T00:42:01.66+00:00

What should I do to rectify this situation?

Thanks.
EmilyS726 264.6K Reputation points Independent Advisor

2026-09-09T00:43:41.75+00:00

If everything is working fine, I think you may not need to do anything. Those folders like you observed, would recreate themselves anyway.

But if you notice things are not working well with those apps, you can always move the files back into its same folders now in OneDrive.
SHV 160 Reputation points

2026-09-09T00:54:23.54+00:00

According to the above explanation, I'm not sure why OneDrive would have an issue, or could even tell, that I moved three local folders from one location to another...

However, I would like to eliminate the recurring message I posted earlier, with a varying number around 500 files.

Suggestions welcome.
EmilyS726 264.6K Reputation points Independent Advisor

2026-09-09T00:57:56.3066667+00:00

Every time you move things into OneDrive folder, it tells OneDrive you want those files synced to the cloud.

Vice versa, when you move anything out of OneDrive folder, it tells OneDrive you want them deleted from the cloud. So, I believe those three folders contain the 500ish files after you moved them out of OneDrive. You can choose delete them. Since you have them in the Document-old folder anyway.

If those apps don't work well after the action above, you can move them back.
SHV 160 Reputation points

2026-09-11T02:23:48.59+00:00

I took your advice and clicked "Delete all items", so I hope it doesn't upset the applecart, but fingers crossed all the same.

Cheers!

Answer 2

This usually means OneDrive still sees a large delete or move operation inside a folder it is syncing, and it is asking for confirmation before removing those items from OneDrive.

In this case, the most likely cause is that the Desktop/Documents backup relationship changed, and OneDrive is repeatedly detecting items that were moved out of a synced location. The three folders moved out of Documents could trigger that behavior if OneDrive still considers them part of the synced OneDrive folder structure.

Best practice is:

Check whether those folders are still inside the OneDrive folder structure.
- Open File Explorer.
- Confirm whether Classin, WeChat, and QQ are now outside the OneDrive folder.
- If a file or folder is still inside OneDrive, moving it outside the OneDrive folder removes it from OneDrive and makes it only available on the PC.
Review OneDrive backup settings.
- Open the OneDrive cloud icon.
- Go to Settings > Sync and backup > Manage backup.
- Check whether Desktop and Documents are enabled.
- If Documents is enabled, changes inside that protected folder are treated as OneDrive changes.
If the goal is to keep certain folders local only, keep them outside the OneDrive folder structure.
- Microsoft’s guidance is that moving folders out of OneDrive makes them only available on the PC.
- Important: files moved out from OneDrive are not backed up or protected. If the computer fails, that content can be lost.
If the prompt keeps appearing, avoid choosing Delete all items unless those deletions are definitely intended.
- Safer choices are to keep the files, then verify folder locations and backup settings first.
If the folders were deselected from sync and the warning is tied to duplicate/existing items, Microsoft’s documented workaround is either:
- delete the local copy from the PC if it is still safely available in OneDrive online, or
- move the folder completely outside the OneDrive folder structure so it is no longer part of OneDrive.

A practical setup for this scenario is:

Keep Desktop backed up only if it is meant to roam across devices.
Keep Documents backed up only for folders that should live in OneDrive.
Leave app data or large local-only folders such as chat/application folders outside OneDrive.
Do not store Outlook data files in OneDrive, because Microsoft states they are not suitable for OneDrive sync and can cause sync problems.

If the warning appears at every startup even after confirming the folders are outside OneDrive and backup settings are correct, sign out and sign in to re-link the OneDrive folder, then select Use this folder when prompted.

References: