2 geth nodes on private network lose blocks when they synchronize

I have been running a private network with two machines connected in various ways - that's not the issue. But they were just running along separately for a few weeks, and each had its own transactions - some contracts were deployed and then were updated on each node while not in contact with the other. When I then turned on both machines and they connected, the resulting consensus just threw away three contracts from one of the nodes. What happened to immutability?? How can that be a proper synchronization result? The contracts are lost even on the machine that originally deployed them. This is not okay.
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