When we remove/replace battery pretty quickly, the voltage on VRTC may not go below 1.4V in a very short span of time. In this case, it may not get an RTC reset. When we remove power, each power supply decays down at its own rate. We have 3 power pins on the module: VIN_3V3, VDDIO, and VRTC. There is also a 1.8V regulator, with its own output capacitors. Each one has its own decay down rate, which also may depend on that the system was doing when power went off (so TX, RX, and idle could differ in how fast the supplies go down.
Our module is not fully protected from all sequences and decay part way down levels.
One thing that might affect things would be to write value 3, rather than value 1 to register 410001AC. This will make the core brownout do an RTC reset, rather than a reset of the core only.