When you convert an old map to a recent version, the loaded world is missing some but not all chests. The same issue was mentioned in MC-70813, and after some tests, I can confirm that the disappearing of chests occurs when moving from 1.7.10 to anything above. Up to 1.7.10, the chests remain with all its content, but past it, they disappear. I tested this using Super Hostile maps after I noticed that some wool chests were missing from the game, and same results were found across all maps (except Iceolation, a 1.12 map). It says the issue has been resolved in MC-70813 but I doubt that's the case.

Testing with same map several time made the same chests disappear. No mods were installed in the previous version - it was vanilla. 

EDIT: The screenshot below is looking at the same chest, one in 1.7 and one in 1.8. The chests still disappear in any versions above 1.7.10. 

1.7.10 world

1.8.9 world