Interfacing Raspberry PI to HoneyWell alarm system (3V vs 12V)
Using a resistor divider for this is probably a bad idea, for a few reasons: ground isolation, electromagnetic compatibility, and whether the 12V output (and I'm assuming it's a 12V output from the alarm system that you're trying to monitor from the Pi) even has a full push-pull topology.

My first guess as to why you always see a 1 is that the 12V output may only a pull-up transistor and no pull-down, so the input pin will just float high.  Or you've chosen the resistor values poorly, or a whole bunch of other possibilities.

The usual approach (unless the data rate is really high, like a Mbit or more) is to use an opto-isolator.  That should get you a clean, isolated, level-shifted signal that can be directly observed by the Pi - you'll need to google ("opto-isolator input pi" or similar) a schematic but there are plenty to choose from.

The second issue is that if those two lines are clock+data outputs from the alarm, you are going to struggle to interpret them on the Pi as GPIO because you just cannot read them fast enough, with no gaps, to ensure that you get every bit.  You would need to connect them to a dedicated I2C or SPI peripheral (whichever is appropriate for the actual signaling protocol coming from the alarm), configured as slave, in order to interpret the bit-stream in realtime without the linux scheduler getting in your way.