Translation:It took three days.
In some cases--including days and dates--Japanese uses special counters for some numbers.
一日（ついたち when talking about the first of the month; いちにち when counting numbers of days）
You also see this at work with general counters, such as when you're counting abstract things.
I don't know the history of this alternate way of counting, but since it's your "escape valve" when you can't remember the specific counter for something, it's a good thing to know.
If you meant that as a question, the answer is "no" (as far as I understand as a learner).
三日, in this context (and any other context), is みっか.
三日間 is みっかかん too.
The only times when it becomes さんにち:
- When it's part of a longer number, such as 十三日 (じゅうさんにち, "thirteen days").
- When it's part of a listed range of days, such as 二三日 (にさんにち, "two or three days").
Whether or not さんにち might be a non-standard variant way of saying just 三日 though, I have no idea. However, みっか definitely isn't incorrect in this sentence. ^^
I was wondering about this, since tups stated mikka was third day, not three days, and 'ka' was added before getsu for duratuon in months, but didnt state it could be used for days...... The audio in this module is making things difficult. Easy to understand the text, but not for prepping us to understand from speech :(