You can track the history of the directory deletion an recreation in the NTFRS outlog per NTFRSUTL OUTLOG >Outlog.txt
For example, directory Test1 is deleted, recreated and morphed via a remote partner.
The old directory Test1 is deleted on member RWVSM2 (OriginatorGuid 60fd3eda-88e0-4da1-a4ceb38e90fdd01c).
Table Type: Outbound Log Table for DOMAIN SYSTEM VOLUME (SYSVOL SHARE) (1)
SequenceNumber : 00028e1e
Flags : 00000028 Flags [Locn LclCo ]
IFlags : 00000001 Flags [IFlagVVRetireExec ]
State : 00000014 CO STATE: IBCO_OUTBOUND_REQUEST
ContentCmd : 00000000 Flags [<Flags Clear>]
Lcmd : 00000003 D/F 1 Delete
FileAttributes : 00000010 Flags [DIRECTORY ]
FileVersionNumber : 00000002
PartnerAckSeqNumber : 00000000
FileSize : 00000000 00000000
FileOffset : 00000000 00000000
FrsVsn : 01c9bda7 456e07bd
FileUsn : 00000000 2e4460f0
JrnlUsn : 00000000 2e4460f0
JrnlFirstUsn : 00000000 2e4460f0
OriginalReplica : 1 [???]
NewReplica : 1 [???]
ChangeOrderGuid : 4b4884b4-254e-4544-b782eb6540010381
OriginatorGuid : 60fd3eda-88e0-4da1-a4ceb38e90fdd01c
FileGuid : b2f62e58-f7fd-4b80-abb24a5cc03539d6
OldParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
NewParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
CxtionGuid : 45beeef3-0863-4097-8d45ec951e3522d4
Spare1Ull :
MD5CheckSum : MD5: 00000000 00000000 00000000 00000000
RetryCount : 0
FirstTryTime : Fri Jun 5, 2009 16:55:32
EventTime : Fri Jun 5, 2009 16:55:31
FileNameLength : 10
FileName : Test1
Cxtion Name : <Jrnl Cxtion> <- <Jrnl Cxtion>\<Jrnl Cxtion>
Cxtion State : Joined
The new directory Test1 is created and renamed on member RWVSM2, with new FileGuid 0cd66c8c-af2c-4376-89e5b77ab1e5b8ef.
Table Type: Outbound Log Table for DOMAIN SYSTEM VOLUME (SYSVOL SHARE) (1)
SequenceNumber : 00028e1f
Flags : 01000028 Flags [Locn LclCo CmpresStage ]
IFlags : 00000001 Flags [IFlagVVRetireExec ]
State : 00000014 CO STATE: IBCO_OUTBOUND_REQUEST
ContentCmd : 00000000 Flags [<Flags Clear>]
Lcmd : 00000001 D/F 1 Create
FileAttributes : 00000010 Flags [DIRECTORY ]
FileVersionNumber : 00000000
PartnerAckSeqNumber : 00000000
FileSize : 00000000 00000000
FileOffset : 00000000 00000000
FrsVsn : 01c9bda7 456e07be
FileUsn : 00000000 2e446300
JrnlUsn : 00000000 2e446138
JrnlFirstUsn : 00000000 2e446138
OriginalReplica : 1 [???]
NewReplica : 1 [???]
ChangeOrderGuid : cda323dd-7a7b-47c0-a882cdc587fb138b
OriginatorGuid : 60fd3eda-88e0-4da1-a4ceb38e90fdd01c
FileGuid : 0cd66c8c-af2c-4376-89e5b77ab1e5b8ef
OldParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
NewParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
CxtionGuid : 45beeef3-0863-4097-8d45ec951e3522d4
Spare1Ull :
MD5CheckSum : MD5: 142e4db1 eee3922a 94c8e76c 9e126531
RetryCount : 0
FirstTryTime : Fri Jun 5, 2009 16:55:38
EventTime : Fri Jun 5, 2009 16:55:34
FileNameLength : 20
FileName : New Folder
Cxtion Name : <Jrnl Cxtion> <- <Jrnl Cxtion>\<Jrnl Cxtion>
Cxtion State : Joined
Table Type: Outbound Log Table for DOMAIN SYSTEM VOLUME (SYSVOL SHARE) (1)
SequenceNumber : 00028e20
Flags : 01000024 Flags [Content LclCo CmpresStage ]
IFlags : 00000001 Flags [IFlagVVRetireExec ]
State : 00000014 CO STATE: IBCO_OUTBOUND_REQUEST
ContentCmd : 00002000 Flags [RenNew ]
Lcmd : 0000000f D/F 1 NoCmd
FileAttributes : 00000010 Flags [DIRECTORY ]
FileVersionNumber : 00000001
PartnerAckSeqNumber : 00000000
FileSize : 00000000 00000000
FileOffset : 00000000 00000000
FrsVsn : 01c9bda7 456e07bf
FileUsn : 00000000 2e446270
JrnlUsn : 00000000 2e446270
JrnlFirstUsn : 00000000 2e446270
OriginalReplica : 1 [???]
NewReplica : 1 [???]
ChangeOrderGuid : 9ad45a1f-6419-46bb-a21fc255b5985f98
OriginatorGuid : 60fd3eda-88e0-4da1-a4ceb38e90fdd01c
FileGuid : 0cd66c8c-af2c-4376-89e5b77ab1e5b8ef
OldParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
NewParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
CxtionGuid : 45beeef3-0863-4097-8d45ec951e3522d4
Spare1Ull :
MD5CheckSum : MD5: 142e4db1 eee3922a 94c8e76c 9e126531
RetryCount : 0
FirstTryTime : Fri Jun 5, 2009 16:55:40
EventTime : Fri Jun 5, 2009 16:55:37
FileNameLength : 10
FileName : Test1
Cxtion Name : <Jrnl Cxtion> <- <Jrnl Cxtion>\<Jrnl Cxtion>
Cxtion State : Joined
During FRS replication the deletion cannot be performed on partner RWVSM1 because the file is locked and new folder Test1 is morphed (remote OriginatorGuid 0fff42a5-d0d5-4fb6-aacd854ea225f0c4)
Table Type: Outbound Log Table for DOMAIN SYSTEM VOLUME (SYSVOL SHARE) (1)
SequenceNumber : 00028e21
Flags : 03100204 Flags [Content OofOrd SkipOrigChk CmpresStage SkipVVUpdt ]
IFlags : 00000001 Flags [IFlagVVRetireExec ]
State : 00000014 CO STATE: IBCO_OUTBOUND_REQUEST
ContentCmd : 00002000 Flags [RenNew ]
Lcmd : 0000000f D/F 1 NoCmd
FileAttributes : 00000010 Flags [DIRECTORY ]
FileVersionNumber : 00000002
PartnerAckSeqNumber : 00001d6c
FileSize : 00000000 00000000
FileOffset : 00000000 00000000
FrsVsn : 01c9c739 e01ec252
FileUsn : 00000000 2e447380
JrnlUsn : 00000000 00000000
JrnlFirstUsn : 00000000 00000000
OriginalReplica : 1 [???]
NewReplica : 1 [???]
ChangeOrderGuid : e294e5b4-2494-4b72-b2060aea700510b7
OriginatorGuid : 0fff42a5-d0d5-4fb6-aacd854ea225f0c4
FileGuid : 0cd66c8c-af2c-4376-89e5b77ab1e5b8ef
OldParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
NewParentGuid : 72a2c009-0710-4f35-b813fb49b43043b5
CxtionGuid : d6946061-6730-4734-a80b1c62fa2677bd
Spare1Ull : Tue Dec 9, 2008 14:59:37
MD5CheckSum : MD5: 142e4db1 eee3922a 94c8e76c 9e126531
RetryCount : 0
FirstTryTime : Fri Jun 5, 2009 16:55:44
EventTime : Fri Jun 5, 2009 16:55:39
FileNameLength : 40
FileName : Test1_NTFRS_c88de319
Cxtion Name : D6267BD6-398D-4FCB-9743-6131CAFBF257 <- RWVSM1\RWR2DOM\RWVSM1$
Cxtion State : Joined
The behavior is per the conflict resolution design of FRS. Even if it happens only together with sharing violations on the deletion target structure, it is not recommended to use folder deletion and recreation as recovery mechanism for FRS folder restore. Morphed directories with in the Policies folder in SYSVOL will have a strong impact on users, who will not be able to read Group Policy information.
Note You may configure FRS to have fewer sharing violations using the following KB article, but this will not help in all circumstances:
816493 How to configure the File Replication Service to allow fewer sharing violations that block replication