Both direct web download and GOG Downloader files of below are broken:

Main Game: Pillars of Eternity II: Deadfire
DLC: Seeker, Slayer, Survivor; The Beast of Winter; Rum Runner's Pack; Beard and Hair Pack; Scalawags Pack; Deck of Many Things
Version: v3.1.0016 (24640)

Please fix these files!

The following files are broken. The file size is too small. The file sizes should be 1.7GByte and 1.2GByte:
setup_pillars_of_eternity_ii_deadfire_-_the_beast_of_winter_v3.1.0016_(24640)-1.bin
setup_pillars_of_eternity_ii_deadfire_-_seeker_slayer_survivor_v3.1.0016_(24640).exe

The following files could be installed on my computer, they are already fixed:
setup_pillars_of_eternity_ii_deadfire_-_prize_crew_v3.1.0016_(24640).exe
setup_pillars_of_eternity_ii_deadfire_-_beard__hair_pack_v3.1.0016_(24640).exe
setup_pillars_of_eternity_ii_deadfire_-_deck_of_many_things_v3.1.0016_(24640).exe
setup_pillars_of_eternity_ii_deadfire_-_vox_machina_pack_v3.1.0016_(24640).exe
setup_pillars_of_eternity_ii_deadfire_-_rum_runners_pack_v3.1.0016_(24640).exe

Plese put the correct files with proper file size in place. Thank you!

There's something wrong with the offline installers for the base game as well.

For example, the first of the bin-files is not the usual 4GB but a mere 291MB in size.

Files are still broken, also no install with GOG Galaxy possible. Please fix this.

Why are there 2 files for the latest update?

Patch (v3.0.2.0027 to v3.1.0016), English
Patch (v3.0.2.0027 to v3.1.0.0016), English

They have different sizes but only the first one works. The second one has an odd extension.

After installing the patch the game doesn't see my DLC's. I had the game version 3.0.2.0027 installed plus all the DLC's except 2 cosmetic ones.

I had to download all of them again. I've downloaded the smaller ones and installed them again. The game can see them now.

I cannot download The Beast of Winter and Seeker, Slayer, Survivor DLC's because the installers are broken.

In addition to the above, the full install is also broken, with the Download sizes, I get matching my browser reported size
setup_pillars_of_eternity_ii_deadfire_v3.1.0016_(24640)-1.bin
291 MB download, should be 4 GB as all full bin files are, only last one is not 4 GB, and that's also wrong

setup_pillars_of_eternity_ii_deadfire_v3.1.0016_(24640)-6.bin
588 MB download, should be 1.4 GB.

I don't know if it will help, but I filed a request about some of these issues with GOG Support.

Patched my game to the latest, and it won't recognise any DLC, and when I try to install DLC it says my game is broken/corrupt.

Try to download the full game on Gog Downloader and it says its broken.

Download of these offline files was successful. Installation, too:
setup_pillars_of_eternity_ii_deadfire_-_the_beast_of_winter_v3.1.0.0016_(24640).exe
setup_pillars_of_eternity_ii_deadfire_-_the_beast_of_winter_v3.1.0.0016_(24640)-1.bin
setup_pillars_of_eternity_ii_deadfire_-_seeker_slayer_survivor_v3.1.0.0016_(24640).exe

Thank you GOG, CD project Red or mysterius Mr. Bug-Fix!