So, I have been playing D2 for about 60h now, and I just realized that I didn't activate the Cross Save when I started to play it on Steam (I had a character on Battle.net when it was available there)
My question is, if I activate it now, will I lose all my progress on my current account?
Or will it save my other guardian in another slot?
If you are referring to pc migration from battlenet to steam, yes. If you migrate your battlenet will overwrite your steam save so you will lose that progress.