@ss9227 At the bottom of the page at the URL opera://settings/content, make sure "Automatically remove permissions from unused sites" is disabled and restart Opera. The setting being enabled shouldn't remove permissions as fast as you're seeing, but maybe the setting is buggy.
Also, make sure you're not clearing "site settings" when clearing things at the URL opera://settings/clearBrowserData.
You can also see if it happens in a test standalone installation. If it doesn't, there might be an issue with your normal installation. For example, it could be due to syncing settings with Opera Sync. Or, it could be permission issues with your profile folder.
To fix permission issues with your profile folder, if you're on Windows, while Opera is closed, in Windows Explorer (File Explorer), with "file extensions" and "hidden items" enabled under "View -> Show", in both "C:\Users\yourusername\AppData\Roaming" and "C:\Users\yourusername\AppData\Local", right-click on the "Opera Software" folder, goto "properties", click the read only box to clear it (so it's all white) and click apply. Then, switch to the "Security" tab, make sure your username is in the user list and make sure it has full control (all permissions set to "allow" except "special permissions"). Click apply if you had to change anything there and OK out.
Your profile could be corrupted. Starting completely fresh with fresh data and settings by closing Opera and renaming the "Opera Stable" folder to "Opera Stable old" in both "C:\Users\yourusername\AppData\Roaming\Opera Software" and "C:\Users\yourusername\AppData\Local\Opera Software", and then going to https://www.sync.opera.com/ in another browser, logging in and choosing "reset passphrase" to wipe out all your Sync data, might fix things.
If it's specific to notifications, in settings in Windows, goto "System -> Notifications" and make sure "Notifications" are on, "Do not disturb" is off, "Turn on do not disturb automatically" is off, "Focus" is off and make sure Opera is listed in the app list below. If Opera isn't there, goto https://cleverpush.com/en/test-notifications/ in Opera and try the "Greetings" test multiple times (and allow it when asked). That should get Opera in the list. With Opera in the list, click it and make sure its settings are all on and correct. Also, in the notification center in Windows, clear any existing notifications from Opera.
Also, make sure you don't have any apps like CCleaner installed on your system that clear things in Opera's profile and cache folders.
You can also uninstall Opera (do not choose to delete your data when uninstalling), delete the install folder afterwards, download the Opera installer in whatever browser you want, launch the installer, click "options", adjust everything how you like and install. That can fix corrupted Opera program files.
Besides all that though, it might just be a bug.