One option:

• Every time an item is unloaded, save the in-game date and time as part of its data.
• Every time an item is loaded that has historical data, check that timestamp.
• Use the time difference between now and then to calculate whether fires have burned out, whether the temperature should have returned to the ambient temperature, etc. You could also assume some kinds of contaminants wear away after a certain time: water dries up, biological substances degrade, etc. If item degradation is ever implemented, potentially you could roll for damage to items that have been unloaded for very long periods of time, although you’d want to know if they were supposed to be exposed to weathering, etc. and you might not have good data on this. Or if food spoilage is ever changed so that items being carried or stored in barrels should still spoil, you can check for rot this way too.

This is how Cataclysm: Dark Days Ahead checks if food has rotted or fires have burned out while you were away from an area.