The scrollback ends up syncing up after the netsplit on both sides of the partition - you see a flood of messages come in from the other side of the split. In the relatively near future the remote side of the split will shown as a thread (if your client supports threads).

Technically, every message you send in Matrix is a mini-netsplit which then resolves as soon as it's received by the other server(s). So you don't tend to notice partitions, unless they go on for minutes on end and disrupt the conversation, but even then the history syncs up afterwards.