Warning: this solution seems to work but I did not test it thoroughly so it may break your game.

SPOILERS AHEAD

There is "an altar quest" on block 6 level 3 where you need two items to use: one is Fire Jewel (found in hidden area of block 6 level 1) and the other is Piece of Coral which should be in case in hidden area of block 6 level 2 - proof: https://www.youtube.com/watch?v=PFqjXmrNaTE#t=1751

The problem: in current version of the game this case is already open and empty.

The only method I found to get this Piece of Coral is to edit the savegame file. I had some saves from before I got Fire Jewel so I was able to do some comparisons.

Three additional text strings appeared in savegame after getting Fire Jewel:
#1. in between <items></items>: 81=1 was added
#2. in between <variables></variables>: FireJewel="T" was added
#3. in between <variables></variables>: FJ="T" was added

I'm guessing that:
#1 is to put Fire Jewel in inventory
#2 is to make Fire Jewel visible for the altar
#3 is to make Fire Jewel marked that we got one copy of it (to prevent getting more)

After using Fire Jewel on altar #1 and #2 were deleted from savegame, #3 was still inside.

After some data searching I've found three corresponding strings for Piece of Coral:
#1: 82=1
#2. Coral="T"
#3: CO="T"

How to implement my solution? If the case with Piece of Coral is also already empty for you and you have already got Fire Jewel then go to altar, save your game and open savegame file in text editor. Now:
#1. find 81=1 between <items></items> and add 82=1 just after it
#2. find FireJewel="T" between <variables></variables> and add Coral="T" just after it
#3. find FJ="T" between <variables></variables> and add CO="T" just after it

When you load this edited savegame you should have Piece of Coral in inventory and it should be visible in altar menu for you to use.

My final thoughts: I think CO="T" string is the core of this bug - even if it isn't in savegame yet, game assumes that Piece of Coral was already taken from the case and used on altar. Why do I think so? When I edited savegame from before I got Fire Jewel and added FT="T" in it, my Fire Jewel case was emptied.

And again, warning: this solution seems to work but I did not test it thoroughly so it may break your game.

Thanks this is so much awesome!

Are the GOG and Steam versions same now? I've got the Steam version. Also does the GOG version really have the KS special summon, Dryad and Succubus?

I do not know anything about Steam version because I don't use Steam at all. To be honest, I don't even have GOG version - I have DRM-free version from Humble Bundle but Humble Bundle does not have forum so I posted my discoveries here and assume that both DRM-free versions are the same. My version has Dryad and Succubus and Giant (but I'm not so sure if Giant was kickstarter-only character).

PS. As I said I don't have Steam but I saw that people have similar problems on Steam forum. Maybe you could post on Steam forum the links to my three guides (two about missing / buggy items, one about game screen resolutions) to help them out also?

Sure thing, I'll do that! :)

Did you help KS the campaign btw? I heard only they had them but somebody was saying the GOG version has them too now.

No, I was not aware about that game at KS time.

Update: I've just finished the game myself with this savegame edit and haven't encountered any visible problems. Have you already posted something? :)

I'm sorry, I was busy and wanted to wait until you confirmed the game worked fine till the very end. That's really great then, you managed to fix what the dev didn't (he did try though, I'm not sure if he gave up or not, the last patch is from May 2015)!

Do you have a Steam account? That way you could get the direct credit for it too! :)

I wouldn't be asking someone else to post if I have my own account. :)

Ah okay. :)

Also, all I am asking is to post links to my posts here on GOG - that way it would be very easy for me to implement any updates in future.

Yeah, I get that. :) Done!

By the way, were the monsters' bugged abilities fixed? I remember that Skeleton had defense broken, which supposedly was fixed by the latest patch but I haven't tried the game with the patch yet. And the vampire had some changes done to his skills, which weren't documented.

Thank you.

It was my first run so I can't compare. Vampire was not in my party - what was changed? Skeleton was in and seemed to work ok, but I don't know what exactly was broken before?

Basically Skeleton has this whole party defense skill, called Barrier or something that adds defense or boosts defense, but it wasn't working properly. I've played it year(s?) before the 2.5 patch came out though.

Also Vampire used to have Blood Leech/Drain, or a similarly named ability that was used to heal him and allies in exploration mode (non-combat). In exchange for as small amount of his HP he healed an ally, however he could use it on himself as well. And he gained more health than he lost by using the ability, it was broken as you had a free whole party heal when not in combat! :D And this ability was either nerfed or removed and instead he gained a new one (I think) and also in combat or leveling up receives something called Vampire blood, but no one knows what does it do, or if they do, no one has posted about it.

The location of the save file on my Mac was in "~/Library/Caches/unity.UltraRunaway.Paper\ Sorcerer"

3 years later, the problem persists, and your solution saved me.
Thank you mate!