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

Lexor: 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.

Wickez: Once I wrap up everything else, I will release this as an unofficial patch with an installer.

Pajama: Thank you - will definitely keep my eye open for this.