Happened to me. I fixed it by reloading previous save, and getting the note from the lake shore in advance, then I could loot chest normally.

Otherwise what happened was I looted whole cemetery, and only then went to the shore, got proper note, read it and went back. When I approached the chest that I previously spotted, but was unable to open due to lack of key, an action text showed up, and then vanished almost instantly, to never show up again, thus leaving me unable to loot the chest. I think it said something along the lines of "unlock" but it was too fast to be sure.

So, you are not alone, but there is probably no way to fix this other than reloading previous save and doing it in different order.

I did read the letter previously.
Later today i'll try to load an older save. Will have to redo a bunch of stuff *sigh*

Download the GOG Galaxy client and repair the game, this fixes 99% of problems. I have done it to "fix" 3 quests that were seemingly bugged.