Hello!
I have exactly the same problem. And also for the third time.
A year ago on Windows, six months ago - on the Sinology DS116.
Two days ago this happened on Debian 9.2 (Sync 2.5.9).
There was a normal reboot of the virtual machine. The shutdown was correct.
After the start, he requests a new identity:
[20171118 07:10:08.838] GS: shutdown
[20171118 07:10:08.885] unregister diskio completion queue with id 1
[20171118 07:10:08.885] Torrent session shutdown: done waiting
[20171118 07:10:08.885] Stopping network threads
[20171118 07:10:08.886] Stopping UDP threads for 0.0.0.0:43119
[20171118 07:10:08.968] Stopping UDP threads for [::]:43119
[20171118 07:10:08.996] Shutdown. Saving config sync.dat
[20171118 07:10:08.996] diskio thread stop, drive_id = 5354007485
[20171118 07:10:08.996] diskio destroy, drive_id = 5354007485
[20171118 07:10:08.996] diskio thread stop, drive_id = 5165816562
[20171118 07:10:08.996] diskio destroy, drive_id = 5165816562
[20171118 07:10:08.996] diskio thread stop, drive_id = 5105521278
[20171118 07:10:08.996] diskio destroy, drive_id = 5105521278
[20171118 07:10:08.996] diskio thread stop, drive_id = 5022623812
[20171118 07:10:08.996] diskio destroy, drive_id = 5022623812
[20171118 07:10:08.996] diskio thread stop, drive_id = 4852457946
[20171118 07:10:08.996] diskio destroy, drive_id = 4852457946
[20171118 07:10:08.996] diskio thread stop, drive_id = 4834938076
[20171118 07:10:08.997] diskio destroy, drive_id = 4834938076
[20171118 07:10:08.997] diskio thread stop, drive_id = 4638700508
[20171118 07:10:08.997] diskio destroy, drive_id = 4638700508
[20171118 07:10:08.997] diskio thread stop, drive_id = 4383625789
[20171118 07:10:08.997] diskio destroy, drive_id = 4383625789
[20171118 07:10:08.997] diskio thread stop, drive_id = 41
[20171118 07:10:08.997] diskio destroy, drive_id = 41
[20171118 07:10:08.997] diskio thread stop, drive_id = 18446744073709551614
[20171118 07:10:08.997] diskio destroy, drive_id = 18446744073709551614
[20171118 07:10:08.997] diskio_controller destroyed
[07:20:25.117] Debug log mask has been set to FFFFFFFF
[07:20:25.117] Features mask has been set to 0
[20171118 07:20:25.158] ZIP: Can't locate [version] in zip, error -100.
[20171118 07:20:25.159] I! Configuration from file "/etc/resilio-sync/config.json" has been applied
[20171118 07:20:25.160] test sha1: AE5BD8EFEA5322C4D9986D06680A781392F9A642
[20171118 07:20:25.160] test sha2: 630DCD2966C4336691125448BBB25B4FF412A49C732DB2C8ABC1B8581BD710DD
[20171118 07:20:25.227] test aes: 0A940BB5416EF045F1C39458C653EA5A07FEEF74E1D5036E900EEE118E949293
[20171118 07:20:25.281] diskio_controller created
[20171118 07:20:25.291] register diskio completion queue with id 1
[20171118 07:20:25.291] PLC[0x0000560ebe21c6e0] binding on 0.0.0.0:43119
[20171118 07:20:25.291] D! 20PeerListenConnection::listen[0x0000560ebe21c6e0][10] bound listening socket 10 to IP 0.0.0.0:43119
[20171118 07:20:25.291] PLC[0x0000560ebe21c170] binding on [::]:43119
[20171118 07:20:25.291] D! 20PeerListenConnection::listen[0x0000560ebe21c170][11] bound listening socket 11 to IP [::]:43119
[20171118 07:20:25.291] UDP: bound listening socket 12 to IP 0.0.0.0:43119
[20171118 07:20:25.291] UDP: bound listening socket 13 to IP [::]:43119
[20171118 07:20:25.291] D! 20HttpListenConnection::listen[0x0000560ebe224240][14] bound listening socket 14 to IP 0.0.0.0:8888
[20171118 07:20:25.304] register diskio completion queue with id 2
[20171118 07:20:25.308] Create diskio thread for drive with id 5269615452, path:
[20171118 07:20:25.308] Create diskio thread for drive with id 4351108565, path:
[20171118 07:20:25.308] Create diskio thread for drive with id 4316136436, path:
[20171118 07:20:25.308] diskio thread start, drive_id = 5269615452, priority = normal
[20171118 07:20:25.308] diskio thread start, drive_id = 4316136436, priority = normal
[20171118 07:20:25.309] diskio thread start, drive_id = 4351108565, priority = normal
[20171118 07:20:25.309] Create diskio thread for drive with id 4358415364, path:
[20171118 07:20:25.309] Create diskio thread for drive with id 4651105100, path:
[20171118 07:20:25.309] Create diskio thread for drive with id 4321785616, path:
[20171118 07:20:25.309] diskio thread start, drive_id = 4358415364, priority = normal
[20171118 07:20:25.309] Create diskio thread for drive with id 4430427224, path:
[20171118 07:20:25.309] diskio thread start, drive_id = 4651105100, priority = normal
[20171118 07:20:25.309] Create diskio thread for drive with id 4739376259, path:
[20171118 07:20:25.309] diskio thread start, drive_id = 4321785616, priority = normal
[20171118 07:20:25.309] diskio thread start, drive_id = 4430427224, priority = normal
[20171118 07:20:25.309] diskio thread start, drive_id = 4739376259, priority = normal
[20171118 07:20:25.333] IPv6 is installed
[20171118 07:20:25.345] VerifyFileWithHash failed on file /var/lib/resilio-sync//sync.dat with status 4.
[20171118 07:20:25.345] VerifyFileWithHash failed on file /var/lib/resilio-sync//sync.dat with status 2.
[20171118 07:20:25.348] VerifyFileWithHash failed on file /var/lib/resilio-sync//sync.dat with status 4.
[20171118 07:20:25.348] Unsupported or empty sync.dat file
[20171118 07:20:25.348] My PeerID: 1055D9412497BF5ED84FF448003DBB0E04AA25B5
[20171118 07:20:25.348] LC: LoadLicenses: there is no pro license
[20171118 07:20:25.356] loaded history: 1000 events
[20171118 07:20:25.357] Joining to the multicast group 239.192.0.0:3838 on interface 192.168.1.16 (eth0)
[20171118 07:20:25.357] Joining to the multicast group 239.192.0.0:3838 on interface 127.0.0.1 (lo)
[20171118 07:20:25.357] Joining to the multicast group 239.192.0.0:3838 on interface 10.10.50.1 (tun0)
[20171118 07:20:25.357] Create diskio thread for drive with id 18446744073709551614, path:
[20171118 07:20:25.357] diskio thread start, drive_id = 18446744073709551614, priority = normal
[20171118 07:20:25.358] Debug log mask has been set to FFFFFFFF
[20171118 07:20:25.358] Features mask has been set to 0
[20171118 07:20:25.359] Scheduler: Apply global rule, download limit: -1, upload limit: -1
[20171118 07:20:25.359] CoreState: Total memory: 3079684096, used by Sync: 10387456, percentage used: 0.34
[20171118 07:20:25.359] message thread start
[20171118 07:20:37.582] NAT-PMP: Unable to map port with NAT-PMP.
[20171118 07:20:56.618] OpenSSL: Loaded X509 trusted CA from "/etc/ssl/certs/ca-certificates.crt"
[20171118 07:25:26.491] CoreState: Total memory: 3079684096, used by Sync: 13201408, percentage used: 0.43
[20171118 07:30:27.145] CoreState: Total memory: 3079684096, used by Sync: 13201408, percentage used: 0.43
[20171118 07:35:26.262] CoreState: Total memory: 3079684096, used by Sync: 13201408, percentage used: 0.43
[20171118 07:36:02.480] SRPEH[undefined]: bad shareID (STATE_BEGIN)
[20171118 07:36:02.480] D! 10SyncTcpReq::set_error[0x00007f38100546a0][19] 103 (SyncEncryptHandler)
[20171118 07:36:02.480] D! 10SyncTcpReq[0x00007f38100546a0]: EOF - error: 103 (SyncEncryptHandler)