I want do a print using multiple filament colors. You know, the old stop at layer height, change filament, restart routine. Well, I tried it last night using simplify3d and I ran into a Z height issue that I think is related to auto leveling. So, after searching here I found this post that I think nails the core issue:
https://forum.lulzbot.com/t/skip-auto-leveling-between-multiple-prints/3030/5
So, has the ability to use the last probe matrix been addressed yet in the stock firmware? Please say yes! 
Second, is there another documented way to do this? If not, this is excellent functionality that we’re all missing out on. As it stands, I think it is impossible to print in multiple colors which is a true shame. Any insight or guidance you can provide is much appreciated. Thanks!
I am just beginning to explore this myself. I’ve seen some impressive results on other Reprap machines so surely it can be done on a Lulzbot as well.
I’ve created a “Pause at Layer” plugin for Cura that extends the built-in Pause at Z plugin.
https://forum.lulzbot.com/t/cura-20-pause-at-layer-plugin/4028/1
Maybe it’s of any help?
This is what I did, it works well, but it is a bit time consuming to set up.
https://forum.lulzbot.com/t/pause-and-change-filament/3761/1
The trick is to make sure you don’t do anything that would clear the leveling matrix. Avoid commands like “home”. As I mentioned in that post, I don’t know if running the printer from Cura works with M0. I use Octoprint to run the printer and it worked there. That test print was somewhat annoying as the black was 2 layers if I remember right… It didn’t give a lot of leeway for things to work right. I found the best option was to prime the extruder and immediately resume. I got a little oozing but it picked off with tweezers easily. Better than the layer not printing properly.