I kept getting this error message when trying to get the update, so I reinstalled the game and still get it. I tried installing other games and they work fine, it just appears to be Hypnospace Outlaw. I even manually deleted all of the files and I'm still getting this error.

Those of us who are on the HSO Discord told the devs about it this morning, and they said they identified the problem and were going to try to get the fix to GOG within the next day. So here's hoping we (finally, after three weeks) will get the proper first patch in the next couple days!

In the meantime, I -think- if you download the installer, that should still work, as that is still listed as version 1.00

Any idea what the patch will update?

I had to reinstall the game completely, an update was not possible, there was always the error "Unknown version".