Hello MISAdmin,
You're correct that the Group Policy client processes policies at logon and subsequently refreshes them in the background every 90 minutes (with a randomized offset of 0 to 30 minutes). Because your preference item is configured with the "Recreate" action, the system deletes the target folder and its contents every time this background cycle triggers, which poses a significant risk of data loss while users are working. While the suggestion to use "Apply once and do not reapply" would indeed stop the background deletions, it is likely too restrictive for your needs because it writes a completion flag to the user's registry (under HKCU\Software\Microsoft\Group Policy\History). This prevents the policy from running on any subsequent logon for that user, meaning the folder would only be cleaned once in the user's lifetime, not every session.
To achieve the behavior of cleaning the folder at every logon but preventing it from running during the background refresh, you need to modify the behavior of the Client-Side Extension (CSE) responsible for Folder preferences. Open the Group Policy Object in the editor and navigate to Computer Configuration \ Administrative Templates \ System \ Group Policy. Locate the setting named Configure Folders Preference extension policy processing. Enable this policy and ensure the checkbox Do not apply during periodic background processing is selected.
This configuration instructs the Group Policy engine to ignore Folder preference items during the 90-minute background interval entirely. Consequently, the "Recreate" action will only execute during synchronous foreground processing, specifically when the user logs on, ensuring a clean environment for each session without disrupting the user's workflow later in the day.
I hope you've found something useful here. If it helps you get more insight into the issue, it's appreciated to accept the answer. Should you have more questions, feel free to leave a message. Have a nice day!
VP