First of all, be aware that 一日 is usually read ichinichi, to count one day, or tsuitachi, when it refers to the first day of a month (as in "April the 1st"). But the phenomenon you spotted in ippi also happens to other words, so let's talk about that.
The simple explanation of ippi is that, when you join a ち (like いち) to ひ, the sequence ち-ひ usually becomes っぴ. So you see, the 日 is using its common ひ reading, after all. It's just that ぴ is considered to be a transformation of ひ (in this case, triggered by ち). More details follow.
The change from ひ to ぴ is an example of a sound change or euphony (Japanese: 音便{おんびん}). There are two important types of sound change which may happen when linking words into a compound:
Sequential voicing (連濁{れんだく}): The first kana character of the second word may get a dakuten ゛ mark. For example, 棚 たな → 本棚 ほんだな. (In linguistics terms, the second word becomes voiced, except if it begins with an /h/, which becomes /b/. That's because /h/ was /p/ in Old Japanese, and a voiced /p/ is a /b/.)
If the kana cannot normally be written with a dakuten ゛, then no sound change happens. Even if it can, sometimes it doesn't change. It's a bit hard to predict when will rendaku occur (see here). Just be aware that it does happen, and with time you'll get a feel for it.
Gemination (促音便{そくおんびん}): When two words are linked, the first consonant of the second word may become doubled (gemini is Latin for "twins"). The doubled or "long" consonants are easier to see in rōmaji:
- 発 hatsu + 達 tatsu → hattatsu
- 一 ichi + 個 ko → ikko
- 真 ma + 白 shiro = masshiro
Gemination is often triggered by the first word ending with a つ or ち. In this case, the trailing つ or ち will become a "small tsu" (that is, the syllable will disappear, being subsumed into the new geminated consonant):
- 発 はつ + 達 たつ → 発達 はったつ
- 一 いち + 個 こ → 一個 いっこ
A sequence of /k/ sounds also gets geminated, with one /k/-kana becoming a small tsu:
Sometimes no character becomes a small tsu; the small tsu seemingly pops out of nowhere:
Finally, /h/-sounds (は,ひ,ふ,へ,ほ) are special. Whenever a /h/-sound gets geminated, it becomes a /pp/ sound; that is, the はひふへほ kana get a handakuten ゜ mark, becoming ぱぴぷぺぽ. (Again, this is because /h/ used to be /p/ in Old Japanese). This is what happened to 一日 as いっぴ, and it happens often for counters starting with 一 いち:
- 一発 いっぱつ
- 一匹 いっぴき
- 一夫 いっぷ
- 一片 いっぺん
- 一本 いっぽん