So let me make sure I understand:
As you can see in this photo (courtesy video posted by OlmecFan25 on youtube.com), the pots in Episode 41 are different from those in Episodes 43 and 44, but the ones in Episodes 43 and 44 are the same. The pots were not smashed in either Episode 41 or 43. Also note that in the photo in the lower right, two keys are present during the Temple Run.
Using these facts, it makes the most sense that no keys were present in the pots from Episode 41 (and the first run of Episode 42), and the key that was meant to be placed inside, instead accidentally ended up being placed in with the second key for the next set of pots (seen in Episodes 43 and 44). The lack of having a key did not affect Episode 41's run, since they did not have to complete the King's Storeroom objective.
Since the Secret Battle Plan (Episode 42) was originally in the Throne Room, the team would have been forced to go from the Pit to either the Observatory or Heart Room, into the King's Storeroom, around the horn, and down to the Swamp; there was no way that the production team would have just had them go down the central shaft to reach the artifact. Therefore, the team was forced to smash the pots in the King's Storeroom in order to advance, but the key was not there. Since it was the first production day with the new director, they were probably short on time and did not have time to retape the run, but instead postponed it to a later date. Therefore, the layout changed between the rest of the episode and the featured run for Episode 42. Since the Throne Room no longer existed in the new layout, the room in which the artifact was located needed to be changed, and the shot of the artifact during the Steps of Knowledge needed to be edited.
Then, since the pots were smashed during the original Episode 42 run, they were replaced for Episode 43. They were not smashed in Episode 43, so they were left for the Episode 44 run, where two keys are found to have been residing inside the same pot... the culprit!
Corollary: The reason that Episode 42 was delayed was that there was a production error involving the key in the King's Storeroom, not that Christina was ill.
Does this agree with what everybody else is thinking, or am I still not understanding the whole idea correctly?