I have more experience with tissue culture than mice, but that's sounds surprisingly similar to passaging tissue cultures over and over [1]. Eventually you get to far out and have to start fresh, going back to stock cells.
[0] https://www.jax.org/jax-mice-and-services/find-and-order-jax...
Just some random expenses I could think of:
1) Maintaining the material to restart the line itself is pretty expensive. Expensive equipment, regular quality control, the scientists doing this maintaining would be relatively expensive. 2) The $17000 referenced in the article are "CRISPR/Cas9 injection to obtain knockout founders" I think?) are custom designed genetically modified mice to start a colony with [0]. More standard human disease-relevant db/db mice (model for diabetes) that I've used before are $500/mouse, as a reference. 3) More cynically, the labs that can actually make use of those $17000 CRISPR/Cas founder mice probably have a continuous flow of millions in funding, so they can charge whatever they want.
[0] https://www.jax.org/news-and-insights/jax-blog/2017/march/li...
Ah, the idea that this is the price before amortizing across thousands of mice is perfectly reasonable.
So, let's say you need 20 female mice for an experiment (e.g. 4 groups of 5). That means that you need to have >40 offspring in order to get enough female offspring. That's at least 7 breeding pairs (assuming you're not harem breeding) and you've got to maintain them for 6-8 weeks until you can use them. That's >$1,000 in breeding costs before you get to the actual experiments.
Some of this is "worst case scenario" stuff that wont apply to most lines. The real reason for the high price is mostly 1) that its expensive to make the transgenic mice in the first place and 2) demand is high enough that they can get away with charging that much.