I agree! I think most of us would think of the song "Big Yellow Taxi":
Don't it always seem to go
That you don't know what you've got
Till it's gone
Just a correction and some notes:
You only know (that) what you had was special once you've lost it!
"What you had" = "it", so there's no need to repeat the subject. I used present perfect at the end to show "the present as a result of the past", although present simple is not wrong.
"To lose it" can also mean "to lose your temper", so be aware there's a double meaning to that phrase.
There's a saying, I think it's a U.S. saying but it might be common to all English-speaking countries:
"You never miss the water till the well runs dry."
I found it in a 1908 book published in the United States but it might be much older.