Regtest: One node nullifying other node's balance
You only see the balance of blocks that have at least another 100 on top. This is because coinbase outputs only become spendable after 101 confirmations (the maturity period).

After the nodes reconnect, and one block is mined by node0, node1's previous chain is reorganized away, and from that point on, both nodes work on the same chain.

However, whenever a new block is mined, the balance of the node who mined the block 100 before that is increased.

It has nothing to do with the nBits bug. This is an actual bug in the software which is being fixed now, but it does not affect you.