Not remove trunk flags when set legacy flags

This change prevents removing trunk flags when set legacy flags. Before
this change when setSettingsLocked is called, it will iterate all flags
under the namespace, and if the flag is not in the updated set, then the
flag will be removed. This will cause a issue for local testing of the
trunk flags. If the trunk flag is set through adb while this method is
called for updating legacy flags, the trunk flag in the same namespace
will be reverted.

Bug: 318744532
Test: adb change a flag, and reboot the device, and check the flag value
Change-Id: If5192c4736605f8cb0a87e49e95167415c1be289