You're right. The use of "nya" is quite confusing for people who are learning Indonesian as this word is used not only to express one meaning. Basically, the use of -nya is for third person. (already answered before) Ayah saya sangat baik. Saya sangat sayang padanya. (My father is so kind. I love him so much) Another is like the one that has been mentioned before. -Nya for specific things. Just like the use of "the" in English But actually this is very informal, sometimes it's considered wrong. I don't suggest this for formal writing. There are also several uses of -nya that are used in informal way. One of them is when Indonesian people use -nya instead of -mu to show a certain degree of politeness This is an example: A woman on the street dropped her wallet. You saw it (you barely know this woman) and tell her: - Mbak, pulpennya jatuh - See, "pulpennya" actually means: "pulpenmu". But it is so common that Indonesian people say -nya to replace -mu just simply to make it a little bit more polite. Other use is for some certain words like: Nyata / Fakta - Nyatanya / Faktanya Translation in English: Nyata = real (Adjective), Fakta = Fact (Noun) Nyatanya = Ternyata / Faktanya= (It turned out that..../ The fact is...) Another example in this case: "Kelihatannya/sepertinya/kayaknya (informal) akan turun hujan = It seems that it will be raining." Kelihatannya/sepertinya can mean: "It seems / it seems like" or sometimes can mean "it looks/ it looks like". Seharusnya/harusnya (shortened)= Should. The meaning and the function is the same with when we use "should" in English, which is to say suggestion or something that you should've done but you didn't. "Saya lapar. Saya seharusnya makan siang dulu" (I am starving. I should have had lunch first.) For this case, it is common to use them both in formal writing and daily conversation. Hope this will help you to understand more about Bahasa :)

Actually nya can be mean as dia: example miliknya= milik dia, kepulangannya, kepulangan dia. But in that case ( supnya lagi ) it doesn't have any specific meaning, it's just a suffix to mention that we want that sup (the same sup) again.

-nya is pronouns that you can use to show possession, like in the word rumahnya (rumah dia), bajunya (baju dia). It also can be used to refers to something like in the 'soup' case, just to make it more specific to the things you are talking about. for example: you see a beautiful house right in front of you, and you say to your friend "rumahnya bagus ya!".

- nya is one kind of afiks (affix). affix : prefiks (prefix), sufiks (suffix), konfiks (confix) and infiks (infix) : - nya it is a pronoun suffix stating ownership combined with basic word which does not change the basic meaning of the word. From being a pronoun that claimed ownership, the unit of - nya can have the function to show something. For example, bukunya means "that book", when -nya serves as a denotation. The use of nya good as pronouns or denotation (not as pure suffix) is very common and about one out of every 14 words written in Indonesian have this unit.