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That's just the thing.
If the caboose is in everyday service, it can't be taken out of service until something happens to it that forces it out of service or it can be taken out of service during the seasonal lull in railroad activity. I was on a geology field camp to Owens Valley in 2006, and even though we were there in June, the passes to Yosemite from the Owens Valley side were still closed. I can only assume then that winter traffic into Yosemite was light, even a century ago, which means winters were for maintenance and rebuilding the equipment. Whatever happened in the winter of 1912, we can assume that either 16/1 was involved in a mishap that required it to become disposed, or 16/1 was found to be in such bad disrepair (during maintenance) that it could not be rebuilt during the off season.
I mentioned Shed as a possible place where 15/1 went after it was sold only because that's what typically happened to railroad equipment after it was sold, particularly with private parties (but we don't know the nature of the party that bought 15/1). The (box)car was used when YVRR bought it and then only used as a caboose for two years before YVRR sold it; based upon 16/1 and 17/1, it may indeed have been in good condition at that time and sold because someone offered a good price or YVRR needed the capital in 1908 but only had use for one less caboose than what they had. It's even possible that YVRR sold off what they considered "excess" in 1908 if they were done with initial construction, to balance the books if anything else. If a locomotive was sold in 1908, it may be easier to track that locomotive than the caboose.
This being said, we don't know who bought it or what they used it for or even why YVRR sold it in the first place. I understand the leaning towards "which suggests that it was old and not worth upgrading," but I don't necessarily agree with that conclusion myself; "old and not worth upgrading" to me means "it has no resale value and is thus turned into firewood (disposed)." To me, sold just means they sold it and we can't surmise condition from that description alone.
In all events, Sold means 15/1 car itself did not cease to exist in 1908 and YVRR could very well have bought it back in 1912 to rebuild after 16/1 met its demise - "Disposed" is a pretty bleak definitive deposition, as too is "scrapped" or "wrecked" or "fire." There is this other possibility that someone bought 15/1 in 1908 and then left it sitting on or near YVRR territory as they set about getting their own affairs in order and then YVRR took it back in 1912 to satisfy a debt on the sale or because it could be considered abandoned on their property and they suddenly needed it to replace 16/1.
We agree that in that era the shops could essentially build an entire caboose from the ground up if they needed to do it - but it's often more productive to start from something half way done than it is to start from scratch. I work in aircraft maintenance, and I know too many stories about maintenance personnel taking panels and parts off those stuffed and mounted aircraft on sticks to rebuild broken parts on a flying aircraft to as recent as this last summer. If the shop needed to build a caboose, and they had a guy in the shop who knew where a caboose might be setting, and it could be had cheap, things change hands quick when need be. What we do know is that the shop did a decent job building 16/2 seeing how it lasted until 1923.
It makes the origins of 16/2 a worthy mystery to say the least. Unless we find more data, you would be correct with your conclusion that we may never know the true origin.
Jack, I have added your book to the Christmas list.