Got an issue with prefabs losing data as well (2018.3.5f1 and bolt 1.4.1) but with prefab variant specifically.
1/ Create a new prefab
2/ Add a flow machine from a macro and fill some variables
3/ Create a prefab variant
4/ Open the prefab variant in prefab mode and change the variables values
5/ Save changes in prefab variant
The variables and macro are removed from the prefab variant.
Variables and macro should be saved in the prefab variant.
Data and flow machine are missing from the instantiated prefab variant in Play mode.
When in PrefabMode, variables and flow machine are missing in the variants. Reverting component to the prefab variant is not saved (see video and yes I save the prefab before switching ;)
I tried changing non-bolt component (Tint on the sprite renderer) and that works just fine :(
Let me know if you can't reproduce this one and I will try to reproduce it in a new project.
Project was started in 2018.2 but has been running with 2018.3 since November.
UPDATE: I copied my project in a different folder and updated it to 1.4.3 and the issue still occurs. I also made sure I was working from a newly created prefab and updated the reprosteps above.
WORKAROUND: I use regular prefabs instead of prefab variant for now but I planned to use that for 100+ abilities and I will need prefab variant at some point.
Customer support service by UserEcho