So I had physical version of W3 and now bought GOTY on sale.
I thought I will just update basic to GOTY, that wasn't the case - I have now two games in the list.
I won't have achivments from basic Witcher playing GOTY?
Can I uninstall basic W3 or that would mean another downloading?

I made copy of saves, but GOTY version found them without anty problems.

If your "basic" W3 is up to date (1.31), you already have the GOTY in effect. The only difference is the installers.

Since the two are separate games, you will indeed need to (or get to, depending on how you look at it) unlock all the achievements again.

If you uninstall the basic version, it won't affect the GOTY version: if you have GOTY ready to play, it'll remain that way even after uninstalling the basic game.

I personally have the basic version + DLCs on Steam and GOTY on GOG, and have had a good time unlocking achievements again. :D

The save game folder being the same for both versions is also pretty handy.

what's the changes between GOTY 2.0.0.51 & The witcher 3 standard edition 2.0.0.52 ?