If you use the mod that resets dungeons this can happen as well, due to the mod. I just saw a 'new' dungeon reset mod go up on thunderstore a day or two ago that allegedly addresses this issue, by preventing the reset if a grave is present. The previous mod doesn't look to have that same grave-marker protection.
(Note, I don't use either mod, but that is what I gathered from reading their details).

Based on the mod description, if a dungeon resets when you have a grave marker 'inside' it takes your grave with it, so it makes sense that if a game update does the same reset the same thing would happen.