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I noticed bookmarks on iPhone, iPad, and Firefox(W10) are all messed up. I manually restored the backups of iPhone/iPad and the bookmaks backup of Firefox. But a little while later they all went back to the previous messed up states.
It appears that backup of bookmarks on the iCloud need to be deleted. Presently if I attempt to turn on iCloud Bookmarks sync, a message says that bookmarks on this computer(W10) will be merged with that in iCloud. How can I just delete the backup bookmarks in iCloud?

I recently had issues with my iCloud bookmarks. On my primary Mac I trashed my Safari bookmarks and then imported my backup copy into Safari from an HTML file. Things have been OK for a number of weeks now across all my iCloud devices.

Edit: hmmm, it appears you don't have a Mac. I think you can use IE instead of Safari to do the same thing.

I am using Windows 10 machine and the internet browsers running on it is Firefox and Chrome. As I indicated above I restored a backup bookmarks onto the Firefox but that is automatically replaced seemingly with that saved in iCloud.

I Googled by search word, "How to delete bookmarks saved in iCloud" and which hit the following:
1. Turn on Bookmarks and update your device. Tap Settings > [your name] > iCloud and make sure that Safari is turned on. ...
2. Check your Internet connection. Open Safari and go to http://www.apple.com. ...
3. Check your account details. ...
4. Restart Safari. ...
5. Turn off iCloud Bookmarks and turn it back on. ...
6. Restart your device.

In 1. above, Safari in my device is presently turned off so that I have to first turn on, then message said the present bookmarks on the device(iPhone) would merge with that in iCloud. I went ahead to let that done.
I do not see any change to be done in 2. and 3.
In 4. I assume Safari means an internet browser which in my case is Firefox.
In 5. I assume it means to launch iCloud app on my W10 and remove check mark on he Bookmarks and put it back on as shown below.
My problem is that after putting the check mark and click on "Apply", then a message prompt says download and install iCloud Bookmarks extension on Firefox even though the iCloud Bookmarks Extension is installed on the Firefox. I tried installing it many times but the same message returned. Another word I cannot turn on iCloud Bookmarks..

I'm not sure what you're trying to do, ultimately, but I think I may have a similar situation. I'm a Windows PC user, and as of about a year ago, an iPhone user. If you just want access to the photos from your phone, without an intermediary Dropbox/etc. kludge, just install iCloud for Windows and uncheck everything. If you tell it to sync photos, it will sync in both directions - it will scan your entire PC for photos to upload to iCloud. I don't want this - mainly the other direction. At first, I checked some things, maybe all three, and immediately I had my Chrome bookmarks from my Windows PC, synced by Google across devices, suddenly showing in Safari on the iPhone (personally I found this useful, once I realized it wasn't the typical MSN Disney AOL Yahoo crap - it looked like new extra clutter at first. Why did I find it useful? Because I prefer Safari to Chrome on idevices). So I unchecked everything, and the bookmarks stayed (which again, is fine with me). I'm guessing that if I deleted them now, they wouldn't come back without once again checking the Bookmarks box in iCloud for Windows.

Some granularity in the iCloud for Windows app would be quite nice.

My iPad's Safari bookmarks is messed up. I deleted bookmarks of iPad Safari but the same messed up bookmarks returned. I think that is what is on the iCloud Bookmarks. My thinking is that the bookmarks on my iCloud need be deleted and let iCloud Bookmarks synced to the bookmarks on my Firefox.
Any suggestions?