> edit: if you're asking about the state of these registers when the code is running
Yes, I'm asking you to read out those registers and post their content here.
Sometimes registers don't contain what you've written into them, for example if you don't obey some (not always published) timing rules. Also, you surely have code which you don't show us, which may influence these registers. The mcu works out of the registers' content, so checking the actual content of registers is the first thing to do before looking into more obscure reasons for some feature not working.
Also, did you verify LSE and RTC are running while in VBAT mode and is the clock to , i.e. were there (missed) alarms during VDD was off?
JW