MSP430FR6989 Watch Dog Timer
This is a special register. The upper byte is not like a regular register where setting it to 0x5Ann will read as 0x5Ann. The user guide explicitly tells you it will read as 0x69nn. Hardware wise in the block diagram for the watchdog, you see the upper byte is a password comparison EQU block. So you never actually write 0x5A to the upper byte, it goes to the comparison mechanism.

The 0x5A is a safety mechanism. The debugger is reading the actual register instead of following your code. The upper byte will always read 0x69 in the debugger.