Well, I hate to play devil's advocate but...
As we're not really in the know about the Japanese market for the most part, I think it could be safe to assume that perhaps they looked at the numbers around the end of the anime and decided that it'd hurt them more than they'd profit off of it. I'm not entirely sure about the international marketplace, but I do know that at least in the US, the First Sale Doctrine holds true - once a person buys a product, i.e. us buying a Shinki, it's theirs and unless there's a contract saying otherwise, the seller's involvement ends. There might be ridiculous and obscene prices for Shinki, but that's all on the used market - and if the Doctrine or something similar applies, that means Konami or anyone else involved in the actual production will even see a cent of it. As demand rises, so does the price in a market where the product can no longer be produced; that's why antiques are so valuable, aren't they?
Maybe there was factory troubles, maybe there were a whole bunch of other things that we could speculate about that we don't know, and maybe not even the die-hard Japanese fanbase knowing. But I'm going to try and look at the numbers here.
From what I can gather, the consensus on the English net says that an average anime episode costs about ~$100.000 USD to make. Ignoring advertisements, promotions, market research and what not for the franchise as a whole, that's at least ~1.2 million USD in the bag. That is a LOT of money, no matter how you slice it. And then you add on the yen, so even taking into account the rough 75 JPY - 1.00 USD back in 2012, that is close to one hundred million yen, for an anime that for all intents and purposes, was not that good, didn't burn up any charts or make headlines, or do much to attract attention and new customers to the brand, at least not as much as it could have or Konami would liked it to.
Assuming Konami were wanting to make a profit off of this, this means that they were aiming to make more than 1.2m USD/100m JPY in the foreseeable future to make up for it. Yes, this is probably an exaggeration and there's likely a lot of things like investments and hard financial math I'm missing, but my point stands. The anime was not something that succeeded, at least in the sense of promoting the franchise and making Konami money. Looking at the Battle Masters games - a typical PSP game (at least as of 2005) cost 900,000 JPY to develop, which is $800k to $900k USD. And again this is ignoring advertising and marketing, which are expensive in their own rights. And they made two of these things, and let's assume for a moment that it takes $1 million straight to make a PC game like Battle Rondo.
2007 - Battle Rondo starts
2010 - Battle Masters is released (~900k USD)
2011 - Battle Rondo ends, Battle Masters Mk 2 is released. Moon Angel (40 minutes total or so) is released. Let's be generous and say half the work was done for Mk2 from the original game (450k USD) and 40 minutes breaks down into two standard anime episodes (200k USD)
2012 - Busou Shinki TV goes on and finishes, with an OVA later (~1,300k USD)
While a gross simplification, this comes out to 2.86 million USD, or as of right now, 292 million yen.
Now, it was also mentioned that Busou Shinki was competing with other products like the figma line. I took a quick gander at them, and well... beyond hitting what's hot and getting an advantage that way, an average figma seems to retail around 3,200 yen give or take. From what I can find of Busou Shinki prices before the hike thanks to the secondhand market, they retailed at more than double that. A figure that's soaring in popularity or is in the public consciousness at the moment, with comparable detail and craftsmanship against a figure that not many people know about and has more of a niche charm to it at double the former's price. Frankly, that's a onesided slaughter more than a fight.
Who knows how much it cost them with this factory thing. But I don't think we need to look at that to realize a possibility that we might not want to. It might have been sustainable before, it might have been rather popular among a decent percent of its target population to have a nice profit margin. But as it seems, at least from here, Konami tried pushing it as hard as they could to stir up interest and get some money flowing, but it failed to meet expectations. The production of new figures and news came to a grinding halt. For the first time prototypes of Shinki weren't released as official products. There has been no effort on Konami's part to push this envelope further in the two years since everything stopped, not even making announcements at festivals. The biggest news we get are diorama things and contests for plush dolls.
It might be on hiatus, it might be simple honest difficulty, but there's an equally good chance that Konami doesn't see the franchise as valuable or viable at this point in time, and thus are quietly ignoring its existence while they focus on what brings in the cash. Because really let's face it - that's the bottom line.