What is the meaning of 的 in "有一天你会明白的"?
In Taiwan, According to dictionary owned by Ministry of Education.
的 can mean:

句尾助詞：置於句尾，表示肯定或加強的語氣。

(助詞 at end of the sentence denoting affirmation, or intensify tone.)
有一天你會明白的它 is not correct. You put 它 at wrong position. 有一天你會明白它的 can be better.