Downloaded this game with GOG galaxy half a year ago.
My game version now is 3.6.44.4046b.
I manually downloaded the update patch Patch(3.6.44.4046b 3.6.48.3268b), when running, it says "Game installaion not found, please reinstall".
How can I fix it?

Have you enabled auto updates? You can enable then check out many games that you don't want auto update.
Did you try to install update in same directory as the game? Sometimes that's the problem.



Other than that, try to contact either the devs (Larian) or GOG support.

You could use Galaxy to install the game. And than run the game without Galaxy(if you don't like Galaxy that is). Problem solved!

Problem is GOG only keeps patches for a single version so if you missed any updates, you will need to redownload the game or change to Galaxy. I cannot understand why we cannot have a pull down menu to get older patches.

^this very much. It may be that you want to stay at a specific version (mod compatibility for instance). They should provide links to all files released for that product.