1. Go to Control Panel and create a new Regular role called "A Regular Role". Set no permissions in it.
2. In a new Tab, go to Site Administration for any site (the default is fine, and is already available).
3. Under Content, click "Bookmarks". Create a new Bookmark.
4. After creation, Click "Actions", then "Permissions".
5. In the matrix, find the "A Regular Role", and click the checkbox for "Subscribe". Notice the Owner role has all Permissions checked. Click Save and close the modal dialog.
6. Switch back to the tab with "A Regular Role", and click "Define Permissions".
7. Go to "Site Administration > Content > Bookmarks".
8. Under Bookmarks Entry, put a check next to "Subscribe", and click Save and Ok to the warning.
9. Switch back to Bookmarks tab. For the bookmark, click "Actions", then "Permissions".
10. Notice that the "Subscribe" permission for "A Regular Role" is checked, but greyed out, unable to be cleared, also notice Owner still has all permissions. Close the modal dialog.
11. Switch back to the edit screen for "A Regular Role".
12. Find the entry for "Bookmarks > Bookmarks Entry: Subscribe" and click "Remove" and accept the warning.
13. Switch back to Bookmarks tab. For the bookmark, click "Actions", then "Permissions".
Expected Result: Removing a permission from the Roles Admin portlet will overwrite individual entities permissions but only for the Role and permission. In this case only the Subscribe permission for "A Regular Role" should be removed.
Actual Results: The permissions for all Roles and Permissions are now cleared.
This issue will probably affect all Resource Block Permission Entities: Bookmarks Entry, Bookmarks Folder, Calendar Booking, Calendar, Calendar Resource
Resource Blocks will (or already have) been removed from master and this is not reproducible in master. It's possible that some of the changes to master were backported after Resource Blocks were removed, creating this issue.
I know this was functioning correctly when https://issues.liferay.com/browse/LPS-73348 was merged.