I have experienced the same sort of problem. (Ender 3, marlin 1.19, BLtouch, Cura 3.6)
I have this stl. I sliced it with Cura 3.6, it looks good and made 1 print.
I get shifting layers.
I tried again, fixed the STL in FReeCad, sliced it with Cura 3.6. I get shifting layers exactly at the same layer and of the same exact amount of shift. The STL looks good when sliced in Cura 3.6.
Trying to see if it was the Y-axis, but shift at the exact same layer twice would be very strange for a slipping pully, I decided to just rotate the STL 90 degrees in Cura 3.6. Sliced STL looks goo