Each partition has an image that can be applied to reset that partition to what it "should" be. Most of the partitions then cannot be modified and have OTA updates work... any modifications would make the OTA fail checks that ensure that the update is safe to apply. This is actually valuable, because the updates are not complete images, they are like a recipe to take the existing data on the partition and write new bits in specific locations. If the existing partition doesn't match the expected image, that could write complete garbage over whatever is actually there.
There are a couple partitions that can be changed, notably the userdata partition, where all your stuff is normally written. If you look at the "return to stock" thread, you'll find a script that has 18 unique images, most of which get applied to 2 partitions each so android can perform online updates. One of these images is "system.img" and the partitions it goes on are system_a and system_b.
0. Make sure you have a good backup of your stuff. (Google actually does a surprisingly good job at this nowadays, at least for stuff from the play store)
1. Find the system.img that goes with your current system version. I have no idea where you can find this for recent updates. When I did this, I returned to the original stock image, before any OTAs, but that only worked because that was what the rest of my system was at. You must have the right version of this image for your phone to have the OTA work, and using the wrong image could prevent the phone from booting.
2. get your phone into bootloader mode and connected to your computer. You can either do this by turning the phone off, and then turning it on while holding volume up, *or* connect it while running normally and run "adb reboot bootloader". You can verify that the device is connected properly by running "fastboot devices". Your device should be listed.
3. run "fastboot flash system_a system.img" and "fastboot flash system_b system.img" You only actually need one of these, but I have no idea how to figure out which one is currently in use.
Standard disclaimers apply... if everything breaks, you can always return to stock, but only by wiping userdata, as far as I know.