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User profile for user: Joseph_S. 
User level: Community Specialist
May 13, 2020 7:10 AM in response to Chromebeetle
Hello Chromebeetle.
Thanks for the clarification. In your example, Folder A is synced with iCloud and Folder B is not. When you move the file from Folder A to Folder B you are seeing the alert because removing the file from the synced folder will delete the file from iCloud. If you don't want the file synced to iCloud you can dismiss the alert.
Have a great day.
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Apr 24, 2020 9:10 AM in response to Chromebeetle
Hello and welcome to Apple Support Communities,Chromebeetle.
If I understand your post correctly, when you try to move a folder from one application to another you see a warning that this will remove the folder from iCloud Drive. I’d like to help.
Some applications automatically save files to iCloud Drive. If you are moving the folders to a different application you may need to manually save a copy to iCloud Drive by placing it on your desktop.
This article will tell you more:
Access iCloud Drive files from your iPhone and other devices
Let us know if that resolves this issue for you.
Thanks for using the Apple Support Communities. Take care.
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User profile for user: amandal80 
User level: Community Specialist
Apr 29, 2020 3:52 PM in response to Chromebeetle
Hello Chromebeetle.
It sounds like it's because it was on your Desktop that you're seeing this alert then. Check out the information about Desktop and Documents in iCloud Drive here:
Add your Desktop and Documents files to iCloud Drive
Moving it will remove it from iCloud because your Desktop is currently synced with iCloud. If you want to keep a copy of it in iCloud Drive, try copying the file instead of moving it.
Cheers.
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User profile for user: Chromebeetle 
Chromebeetle Author
User level: Level1 4 points
Apr 30, 2020 10:08 AM in response to amandal80
Thanks for the reply! But I don't really care about having the file saved to iCloud or anything, I just want to make sure the folder actually appears in the file I want it to when I move it in. I guess a better explanation is I want to know why I receive a pop-up that I'm deleting something when I'm not. My problem is:
I'm trying to move Folder A from desktop into Folder B, which is in the Library. I'm doing this because in the application I'm using, Folder B is where my downloaded content goes into. However, when I open the application that lets me see into Folder B, Folder A appears physically there, but does not appear in the application. This does not seem to be the application's problem, as this happens with all my other folders in my Library. I've watched videos demonstrating this exact process online, and the only difference from their process and mine, is that pop-up. So basically, I just want to know why that pop-up might occur when I'm not deleting a file, especially in this scenario, if it makes sense.
Thanks!
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User profile for user: Chromebeetle
Chromebeetle Author
User level: Level1 4 points
Apr 26, 2020 6:15 AM in response to sterling r
Hello! I've put it on the desktop before but the same pop-up happens when I try to put the folder into another folder in the Library. I also cannot upload the folder to iCloud.
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