You don't have to do that unless both platforms save on the same folder,
that they don't on standart,
one of them saves on game folder of your pc user profile
the other saves the game saves within the platform folder under games and
then the specific game.

give it a try, on definitions see where they save the games/user profiles

I will have to take your word on it for the time being.

I know the GOG build saves the profile and the self-destructing save file to the %user%/My Games/FasterThanLight path and that's what my worry was about the Steam build.

Some games, even in the current time, still get weird like that and will just save some things like the profile and temporary save to the same paths despite the developers making separate builds per distribution platform (I assume because it's easier or simpler than coding in new paths for each platform but I am not a coder in any sense of the word so that's merely a wild and likely inaccurate guess).

If the Steam build keeps the save data in a completely different path and doesn't read from GOG's path then it's good to know I won't have to worry about cheesing the achievements in Steam when I decide to take a run at them with that build of the game.

Is there a new secret achievement?
I can't understand if it's one of the old ones or not..

Eh, it's literally called "Secret Achievement" and it doesn't have an icon, at least on my list (you can find it in Galaxy, in the "my Progress" tab)
I don't know if it's just a 100% achiev, because I still miss other 3.
I haven't managed to find info about it online, so far.

Sorry but this wiil have to be a Loonng one;

It should be the secret area then, named:
Ancestry-Find the secret sector with the rock ship,

You will have to grind a good bit, while using a rock ship,
a event will pop up with a crio chamber in space,
pick it up, get to a zoltan sector, find a 2sd event,
this one a scientist will ofter to defreeze the guy,
its a crystal, that should lead you to a rock sector,
with a new event to the crystal secret sector.

Honestly its a nigthmare to get it, is my only one left.
There use to be a cheat code arround it,
where you would name a crystal 1 specific name
at the start, and so cutting in half the task,
but they patch it out i guess.

Good travels and all the luck to get this one.

It's not that tho.
I can see the missing Ancestry achiev in the list.
(and btw yeah, I failed to find it so far, even with the crystal crew)