It doesn't write the file until the server saves or you Unload the plugin. 

Ok
Now it crashes the server after save. Complete shutdown and i had to restart the server.

15:23 [Info] [Sync Pipes] Save v1.0 starting
15:23 [Info] [Sync Pipes] Saved 5 pipes
15:23 [Info] [Sync Pipes] Saved 6 managers
15:23 [Info] [Sync Pipes] Save v1.0 complete (0.291s)
15:23 [Info] [Skin Shop] Saving Skin Data: 0 players
15:24 [Info] [Advert Messages] Das Spielmenü öffnest du mit <color=#9b9c9a>/menu</color>
15:28 [Info] [Economics] Saving balances for players...
15:28 [Info] [Sync Pipes] Save v1.0 starting
15:28 [Info] [Sync Pipes] Saved 5 pipes
15:28 [Info] [Sync Pipes] Saved 6 managers
15:28 [Info] [Sync Pipes] Save v1.0 complete (0.285s)
15:29 [Info] [Skin Shop] Saving Skin Data: 0 players
15:29 [Info] [Welcomer] Spieler ..... hat den Server verlassen. Grund Kicked: Unresponsive
15:32 [Info] [Advert Messages] Die ersten Shop Kategorien sind verfügbar! Schreibe <color=#9b9c9a>/shop</color> oder <color=#9b9c9a>/menu</color>
15:33 [Info] [Economics] Saving balances for players...
15:33 [Info] [Sync Pipes] Save v1.0 starting
15:33 [Info] [Sync Pipes] Saved 5 pipes
15:33 [Info] [Sync Pipes] Saved 6 managers
15:33 [Info] [Sync Pipes] Save v1.0 complete (0.307s)
15:33 [Info] [Skin Shop] Saving Skin Data: 0 players
15:36 [Info] Loading Oxide Core v2.0.4004...

Merged post

I have installed an two days old backup because i installed some plugins yesterday. Problem with player kick was gone. Than i installed only pipes again and kick after some minutes. Found this now in log folder

[SERVER v1.0.20] Started as service
[SERVER v1.0.20] Running as service
[SERVER v1.0.20] Got Message: Ready
[SERVER v1.0.20] Got Message: Compile
[SERVER v1.0.20] Console: SyncPipes.cs(2134,17): warning CS0219: The variable `handled' is assigned but its value is never used
SyncPipes.cs(3646,45): warning CS0414: The private field `Oxide.Plugins.SyncPipes.Pipe.PipeFightOffset' is assigned but its value is never used
SyncPipes.cs(4867,32): warning CS0414: The private field `Oxide.Plugins.SyncPipes.PipeSegmentBase._parent' is assigned but its value is never used

[SERVER v1.0.20] Connection closed.
[SERVER v1.0.20] Shutdown