So, in my case, I experienced a similar wiping issue with a set of Blueprint struct types. I was led to this thread, because my structs was inside a Primary Data Asset, which I considered at first the most probable cause (turns out I was wrong).
My setup was that I had a Blueprint Struct (type A) which contained an array of Blueprint Structs (type B), themselves had an array of Structs (type C) as one of their struct member.
This kind of setup, while it doesn’t trigger any warning in the editor, caused the whole content of the struct (Type A to C) to be wiped out when the editor restarted. I assume it is due to nested arrays.
The solution is to introduce a new type, a fourth structure (kid you not), as a buffer between type B and C.
So now, the final architecture was:
Wrapper Struct type A->Array of Struct type B->Subwrapper Struct type C->Array of Struct type D
This kind of design can be useful to make dialog trees, albeit slightly inconvenient.
So if part of your struct or array get wiped out in or out of a Primary Data Asset, I suggest examining whether you have an array of struct, who themselves have an array of struct as member. If so, it may be a bug in the engine? I don’t know.