In the next step, after the page where you have the problem, there is a step for uploading a scan of your passport in PDF format. In that step, upload a 2-page PDF. The first page can have the scan of your passport. The second page of the PDF can have a letter explaining the issue and naming all the countries.
In the previous page of the application, in the box for countries visited, include a reference to this uploaded page.
Before doing this, e-mail the help desk to make sure it's alright. If they say it is, then start the letter like: "Sir or Madam. As discussed with the help desk..." On the other hand, if they tell you to do something else, then, of course, do that.
You can reach them at email@example.com.
I had the same problem while applying for a regular visa (I've never applied for an e-visa) a couple of years ago, and I got an official response from the company the Indian embassy had outsourced the visa application process to in Australia.
In the "Countries visited in the last 10 years" section, there is not enough space for all the countries I have visited. What should I do about this?
The reply was:
You may provide a covering letter with the details of countries.
The time when I got this answer was not the first time I had the problem. Actually, I've been in this situation all seven times I've applied for a visa to India. Sometimes I've written a supplementary letter with the countries, sometimes I've used abbreviations in the box (US, UK, DK, SL, etc.) I've always gotten the visa, and have never had any questions asked regarding that particular section.
Although it's extremely unlikely that the person processing your application will even notice or know if you leave out a bunch of countries, I'm not personally inclined to do that. I don't like taking such risks at all.
If doing this, though, consider consistency with details from all sections of past and future applications, as well as passport stamps, etc. But as I said, I don't prefer this approach.
Going to extra lengths to be truthful in your application gives a good impression to the person processing it. This is especially helpful if one is in a situation where there's a thin line between getting accepted or rejected. (I'm not suggesting this is the case for you, Mark, but I'm more talking in general to some of the people who may have the same problem in the future. There are likely a lot of people who will indeed have this problem.)
I'd also like to add that from my experience of several instances of applying for visas to India, I've found that it's better to get every single detail right. It's not always so, but in some cases, even a small detail being wrong can cause problems. Personally, I always like to make sure that every single detail in my application is correct before submitting it.
And Mark, as a long-term resident of India, I want to welcome you, and I hope you enjoy your trip!
TL;DR: After having e-mailed the help desk to verify the idea, make a 2-page PDF containing both your passport and a letter regarding the countries and upload it in the passport section. Make every single detail correct.