Controlling that ammonia production is part of affinage. Basically, the faster things are growing on the outside, the faster ammonia will be produced. Ammonia soaks into the cheese, but it takes times. So if things are growing like gangbusters on the rind, the ammonia will pool up just under the rind and you will get a runny paste there as well as a strong ammonia odor.
One of the things you want to do is to control the geotrichum growth on the rind. This is why it's a bit of a tradeoff when you are making the cheese. If you add some geotrichum to the milk, it will get an early start and control other molds for you. On the other hand, it might just grow too fast. I tend to have mixed feelings about this. I've played with adding geotrichum directly to the milk or spraying it on my cheeses, but honestly I tend to prefer having it show up naturally (and I slightly prefer my wild source better than the variety that I bought). It gets a slower start and therefore the cheese can mature a bit more before I have to really think about controlling geotrichum.
And again, b. linens also produces ammonia. So you kind of want to time when that's all coming together. In some ways, waiting longer is nice because you get some proteolysis happening in the cheese to produce flavour and paste texture before you start dumping ammonia in there. That's one of the reasons I tend to prefer the "wash whenever something blooms" over the "wash alternating sides every day" approach. For a washed rind (not alpine rind), it's going to produce a subtly different cheese.
But, for instance, if geotrichum is going crazy, you may want to change your mind and wash early to get b. linens up as soon as you can and then lower the temp to 6 C. Because otherwise in addition to the geo dumping ammonia, it will be producing a lot of geo-funk flavours. I personally like my washed rinds to be simpler. But I've found that if lower the temp before the b. linens shows up, then it takes too long to mature and doesn't really give you the b. linens characteristics.
And then, of course, the longer you grow b. linens, the more ammonia you will produce, which really limits the the lifespan of the cheese. So there is a hard limit to the extent that you can age it (depending on how you approached the problem).
After trying it about a bazillion different ways (and making a *lot* of washed rinds that I didn't really enjoy), my "ideal" practice is: 24 hours or so to dry off the rind at room temps, 16 C and ~80% humidity until geo blooms or at least until it gets "greasy" (depending on the humidity) (up to a week), 13 C and 80-90% humidity washing every time something blooms, as soon as b. linens has coloured the rind move to 6 C and wash occasionally depending on the condition of the rind. I try to aim it so that I get the colour of the rind and the condition of the paste to the right level right at the end of aging.
But it must be said that this is all really subjective and highly dependent upon your actual setup, climate, cheese styles, etc. Also, lately I've been playing with the commercial FR22 b. linens culture and I *really* like it. It's got a nice red colour (my wild one is *very* orange) and I find that it has a bit less bitterness than my wild variant. However, for alpine style (or tomme style) rinds where I'm drying off the rind, I prefer my wild one. It's got the most amazing flavour once the rind has dried off.
Having said all that, affinage is an art. It just takes a lot of practice and experimentation to find the process that works for you. I've been amazed at the difference in the final cheeses as well. The exact same make with different affinage makes a completely different cheese.
