I am aware of chests emptying when you upgrade/downgrade. I don't think this is the same problem because chests in unloaded chunks weren't affected. Hence why I only lost my inventory in the recent upgrade/downgrade glitch, not any of my stuff back at home base. These minecart chests should similarly have been unaffected.
Anyway, I am exploring a new abandoned mineshaft. I might just have been very unlucky, but all four of the minecarts with chests I have found so far have been completely empty. Theoretically possible, but it stretches probability. The chunks affected were spawned many weeks ago, but I have only been in the actual mineshafts since upgrading to 14w18b.
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What you describe are the symptoms of MC-45009
the id's in any chests, or minecrafts etc. are turned to the string id and when you downgrade minecraft doesn't know what it is, and removes is from the world, upgrading back doesn't change that