Here is step by step for quick reproduction:
1. Create new object, make it a prefab
2. Make a prefab variant of the prefab
3. Add fsm to original prefab, add 3 float variables: var1, var2, var3 - check inspector for all. Save
4. Open variant prefab and add values to the variables from the inspector. I used value 1, 2, 3. Save
5. Go to original prefab, delete var2 from the fsm (so it's the middle variable in order). Save.
6. Now go back to the prefab variant, notice var3 now actually have "2" as value - which was the value set var2(which we deleted) originally.