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That is odd. From the fact that it is not available for the whole bag i'm a little suspicious that the connection is getting dropped for some networking/kernel reason. We don't have robust reconnect logic for broken tcp connections. For that problem the workaround that can force a reconnect is to bring up a new publisher on the topic which will cause the master to notify all subscribers on the topic and they will attempt to connect to all publishers, both the new one and the one with the broken connection.
Related to that how are you partitioning your bags? Are you restarting rosbag or is it partiioning the bags based on size inside a single run?
If you have some extra space/bandwidth for logging you could turn up the roscpp logging level for rosbag to debug or superdebug which will give you details about the connection states etc on rosout.
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