Thanks for the reply.
AD Schema is not extended on the new domain.
I've added entries for the new domain In AD Group discovery, system discovery and user discovery. (and this worked).
The inboxes seem okay to me (my experience tinkering in here is quite limited, so I've pasted the counts below):
PS C:\Windows\system32> Get-ChildItem "E:\SCCM\Microsoft Configuration Manager\inboxes" -Recurse| where {!$_.PSIsContain
er} | Group Directory | Format-Table Name, Count -AutoSize
Name Count
---- -----
E:\SCCM\Microsoft Configuration Manager\inboxes\AIKbMgr.box 1
E:\SCCM\Microsoft Configuration Manager\inboxes\auth\dataldr.box\BADMIFS\DeltaMismatch 53
E:\SCCM\Microsoft Configuration Manager\inboxes\auth\dataldr.box\BADMIFS\ExceedSizeLimit 27
E:\SCCM\Microsoft Configuration Manager\inboxes\auth\dataldr.box\BADMIFS\NonExistentRow 6
E:\SCCM\Microsoft Configuration Manager\inboxes\auth\dataldr.box\BADMIFS\Outdated 1
E:\SCCM\Microsoft Configuration Manager\inboxes\auth\statesys.box\corrupt 9
E:\SCCM\Microsoft Configuration Manager\inboxes\auth\statesys.box\incoming 5
E:\SCCM\Microsoft Configuration Manager\inboxes\ccrretry.box 1
E:\SCCM\Microsoft Configuration Manager\inboxes\certmgr.box 8
E:\SCCM\Microsoft Configuration Manager\inboxes\clifiles.src\hinv 1
E:\SCCM\Microsoft Configuration Manager\inboxes\COLLEVAL.box 1
E:\SCCM\Microsoft Configuration Manager\inboxes\ddm.box\data.col 1
E:\SCCM\Microsoft Configuration Manager\inboxes\distmgr.box 10
E:\SCCM\Microsoft Configuration Manager\inboxes\hman.box\pubkey 1
E:\SCCM\Microsoft Configuration Manager\inboxes\objmgr.box 6
E:\SCCM\Microsoft Configuration Manager\inboxes\offermgr.box 38
E:\SCCM\Microsoft Configuration Manager\inboxes\pkginfo.box 164
E:\SCCM\Microsoft Configuration Manager\inboxes\PkgTransferMgr.box\UID 1
E:\SCCM\Microsoft Configuration Manager\inboxes\policypv.box 5
E:\SCCM\Microsoft Configuration Manager\inboxes\polreq.box\bad 2
E:\SCCM\Microsoft Configuration Manager\inboxes\schedule.box\outboxes\LAN 1
E:\SCCM\Microsoft Configuration Manager\inboxes\schedule.box\UID 2
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\BADSinv 6
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16777480 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16777850 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16777922 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778029 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778280 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778391 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778409 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778607 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778650 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778706 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778709 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778719 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778772 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778809 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778875 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778911 2
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778930 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778936 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778937 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778939 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778941 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778952 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778954 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778980 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778981 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778982 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16778997 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779230 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779246 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779565 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779724 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779726 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779727 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779740 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779762 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779766 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sinv.box\FileCol\16779769 1
E:\SCCM\Microsoft Configuration Manager\inboxes\sitectrl.box 1
E:\SCCM\Microsoft Configuration Manager\inboxes\smsbkup.box 1
I expected that the object in SCCM would update with the current domain. The results were mixed. After the updating the discovery, the members in the device collection didn't update their domains, but querying the hostname in devices showed the correct result. Since SOME did update before the discovery, it's seems an awful like a bug to me.
thanks for your help and guidance.