I don't know how practical it is, but unless you destroy the molds the second you retire the line, you could always consider the option of a secondary line for by-order production in the less-than-satisfactory kits, Especially for the ones that are modifications of existing tank lines that are still in your production run, such as the TOS-1, where it's two sprues that you produce in addition. If I'm not mistaken, the molds are seperate of the injection machine, so if you retained the molds and did limited production runs, perhaps it might make an alternative option.
Another thought to mind would be stockpile a small unit of the altered sprues to one side, a limited stockpile at best, maybe five or six or however would satisfy a small limited production run, rather than the full box taking up additional space in the warehouse, set it aside.
It's just a shame that I've got to gamble now and pray that I can get the money in time to get the kits I want if they're to be put out of production, or already are out of production.