XBee S2C fails communcation at some point

I have the following setup:
A: 1 x Coordinator connected via USB dongle (sparkfun) to a Windows 10 IoT device - Serial communication
B: 1 x Router connected to an Arduino Fio
C: 1 x Router connected via USB dongle (sparkfun) to Windows 10 to XCTU
All above are API mode 1.

My scenario is as follows:

I send at each 5 seconds a 6 byte message from A to B and C.
B is instructed to reply to that message with another one of the same size.

After some time, typically 40 - 50 minutes, A no longer receives messages from B.
Reads from Serial port are working (Transmit Status messages are received for each message Sent by A).
C receives messages as seen in XCTU.

If nothing changes A will never hear from B again.

However if (by some internal logic) B sends a message to A or if C sends a 6 byte message (same as the one A sends to B and C) to B, suddenly A starts receiving messages from B.

Why is this happening?

Does anyone know if I can somehow see if something is actually sent over the air between 2 XBees?

It was the arduino library that we misused.
It only works in API Mode 2 and we have the module configured for API Mode 1.
(does anyone know why the library has not yet been updated to be used with API Mode 1?)

It was happening only after a while since we have an incremental counter in our message and at some point, that counter reached a value that contained a special character from API Mode 2 perspective.

From XCTU was always running since there was no incremental logic in there.

I used a digital analyzer for connecting to XBee In and Out pins so to be able to say if it sent something to Arduino or not. One only need to connect to those 2 pins, set the Async serial mode and will be able to see bytes going back and forth.