Please can you attach your test Flowcode project file and resulting .txt log file

Are SDI and SDO the wrong way round?

Try a C code icon with

Just to add to Martin's comment, a look at the datasheet indicates that A9 could be added to the fcd for SPI2 CLK, but not A12.
edit: The circuit diagram shows port C pin 12, using SDIO interface, which Flowcode doesn't support.
Suggest trying software SPI mode?

Hi Brendan,
I am not getting any hang.
Could you attach a sample program that demonstrates the issue?
For example, are you initializing the UART component?

I think the issue here is that you shouldn't mix interrupt driven comms with a polled timed loop.

I've put the code into the CAL file (STARM_CAL_RTC.c)
this goes into directory...
C:\ProgramData\MatrixTSL\FlowcodeV10\CAL\STARM\
This will avoid the need for the extra C icon code.
Note that if you swap between LSI and LSE you need to cycle all power

I found a little time to play with STM32F DFU programming via the USB bootloader, this avoids needing the ST-link programmer. This has been tested with a WeAct STM32F411CE 8MHz Black Pill dev board. First install the STM32CubeProgrammer from www.st.com (at default location) Here's an FCD with modifi...

Looks like this board has a BOOT0 switch, so yes you should be able to program it in DFU mode, via USB, UART.
Flowcode does not support this directly, but the compiler output can be used with STM programing tools such as DfuSe. Also have a look at STM32CubeProg from st.com