Looking through the logs, you can see a save attempt at 8:23 and the following exception taking place. 
Then when a subsequent save was invoked, all pipes were gone at 8:44.

08:23 [Info] [Sync Pipes] Save v1.0 starting
08:23 [Info] [Sync Pipes] Saved 171 pipes
08:23 [Info] [Sync Pipes] Saved 194 managers
at Oxide.Plugins.SyncPipes+DataStore1_0+<BufferedSave>c__Iterator0.MoveNext () [0x00288] in <8f9a5430648d489b9351c6e24bf6e009>:0
at Oxide.Plugins.SyncPipes+DataStore1_0.Save (System.Boolean backgroundSave) [0x00084] in <8f9a5430648d489b9351c6e24bf6e009>:0
at Oxide.Plugins.SyncPipes+DataStore1_0.Save (System.Boolean backgroundSave) [0x00084] in <8f9a5430648d489b9351c6e24bf6e009>:0
08:44 [Info] [Sync Pipes] Save v1.0 starting
08:44 [Info] [Sync Pipes] Saved 0 pipes
08:44 [Info] [Sync Pipes] Saved 0 managers
at Oxide.Plugins.SyncPipes+DataStore1_0+<BufferedSave>c__Iterator0.MoveNext () [0x00288] in <00223962b391464395634bd83fbded84>:0
at Oxide.Plugins.SyncPipes+DataStore1_0.Save (System.Boolean backgroundSave) [0x00084] in <00223962b391464395634bd83fbded84>:0
at Oxide.Plugins.SyncPipes+DataStore1_0.Save (System.Boolean backgroundSave) [0x00084] in <00223962b391464395634bd83fbded84>:0

This looks very odd. Looks like something corrupted the memory store of pipes during the first save.
I'll see if I can work out what caused it.

Has this happened more than once?

it happened with jpipes about a month ago as well.  the main reason I moved to syncPipes :)
this is the first time it has happened with syncPipes, but I've only been using them since the latest wipe.  

if it made a copy of the data file prior to each save or something like that, we could just roll back to it- not sure if that is even possible and just an idea.