Whilst not a complete answer, as I cannot tell retrospectively what caused you to lose boarders, but a couple of points that might be relevant:
If you added boxes but didn't add troughs / showers for each, that could reduce comfort level and make it less attractive for new boarders.
You could board more of your own horses to improve your capacity level, keeping just a few boxes open, to improve your overall prestige and attractiveness.
If you have high skilled horses to board, that will improve the boarder prestige considerably. Otherwise board your own low skill divines, which will help capacity without affecting the skill component.

As encouragement, you have the bones of a great EC. Although it's small, you have good offerings. Offering places in your EC rarely brings in more money than it costs you in bedding, food, free tack etc, so financially you are probably gaining by having fewer boarders anyway! Focus on quality rather than size, and use it yourself too.

In addition to Suzanna's excellent answer, were they all primary the same player or lots of different ones?

If it was only a few players it may be that they had boarded a load of filler horses all around the same time so they all dropped out on the same date. I tend to board my fillers en masse every 100 days or so as I try to find the longest cheapest board with my requirements

Thanks both, these are really kind answers.

It was like 3-5 horses per player, so still around 20 different people, and I actually added more showers and troughs when I put in the new boxes, therefore I still don't understand the exact cause. However Suzanna is right, I'm not doing it for the money, and if other people haven't also experienced it then I'll just assume it's random chance.

Following your advice I'll try boarding my high level horses, and then at least they'll have a nice cozy (and free) place to be boarded whilst I try to build it back.

Thanks again