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Languages like japanese have different pronunciations for each character (in the kanji system in this case) , a kanji character can have up to 20 different pronunciations depending on the the word it is in. Is there or was there any language where each character is pronounced differently depending on the word it's in?

It is unlikely that in some language's writing system, each and every character is pronounced differently depending on the word it's in. For that to be true, it would mean that every character has at least two pronunciations. The implication of "what word it is in" is that what determines the pronunciation is the word, and not the general context (for instance, the Devanagari letter त is pronounced differently when it is combined with the letter ि). Kanji may have multiple readings, for example 明 can be myō or mei. Chinese also has multiple readings for a character. But not all characters are like that.

A candidate for such writing is the Phoenician alphabet, which (originally) only marked consonants, though of course the language did have vowels. So "𐤋" could represent [la, li, lu, l] and you would just have to know what the word is. But this is quite different from the situation with readings for Chinese characters. Still, it might be the kind of thing you are looking for.

There is, as a matter of fact!

Cuneiform was a writing system developed for the Sumerian language, then adapted for Akkadian, Hittite, and many other languages. But the adaptation process was not particularly consistent. Take this Sumerian glyph for example:

It originally meant the words an, "heaven", or An, "An, the god of the sky". But through synecdoche it could also mean diŋir, "deity". And when cuneiform started being used for sounds instead of words, it also meant the syllable /an/.

Then the Akkadians started using the writing system. In Akkadian, this sign was used for the words il ("god"), or šamû ("heaven"), taken straightforwardly from the Sumerian meanings. But, it could still be used for the syllable /an/ from Sumerian, and now for the syllable /il/ from Akkadian!

In fact, some signs, including this one ("DIŊIR", written in capitals to indicate the sign as opposed to any particular interpretation) could also be used as determiners, and not pronounced at all! When written before a name, this sign indicates that it's the name of a deity. This is mostly used for clarifying the huge mess of homophones created by this system.

It is the case in French. Such a differentiation is due to two distinct phenomena: assimilation & polyphonic letters.

An example of assimilations in French:

shop is transcribed in French "magasin" and is pronounced [maɡazɛ̃], but the word "oursin" is pronounced [uʁsɛ̃]. So the letter s can be pronounced [s] or [z].

An example of polyphonic letters in French:

The word "garage", meaning garage, is pronounced [gaʀaʒ]. This example shows that the letter g corresponds to two sounds [g] and [ʒ].

That can be generalised to other languages with old written traditions as English, Spanish and so on.

Let us add, ideograms (such the Kanji) are not an alphabetic writing system. Then, there is not relation between the characters and the signifier, instead the symbols are tied to the signified.