Did any of these countries ever have written languages before that just aren’t known or written anymore?
Define "known"? Do you mean not known by the average person in those countries? Or completely indecipherable to anyone the way that hieroglyphics were before the discovery of the Rosetta stone and the way that Linear A is still undeciphered?
If you mean the former, among countries/languages that currently use a Latin script, Turkey wasn't colonized by Europeans but adopted the Latin script in the 1920s upon the foundation of the republic. Prior to that, Ottoman Turkish, which is a somewhat distinct literary form of Turkish from contemporary Turkish, was written in a modified form of the Arabic script. Knowledge of the Arabic script in Turkey today is limited. Anyone who does a history degree in Turkey as I understand it has to take Ottoman Turkish lessons, and there a large and growing number of religious schools teaching Arabic. But in general your average guy on the street probably can't read the Arabic script.
Separately, prior to the adoption of the Arabic script, there was the old Turkic alphabet. That would probably be about as well known in modern Turkey as Anglo-Saxon runes would be in America.
But it doesn't qualify in the second definition, insofar as it has in fact been deciphered.
Tagalog was formerly written in Baybayin, a script ultimately of Indic origin. The Spanish found it's use widespread enough to use it in their religious materials in the late 1500s (Jason Lobel's dissertation, p 33-34). An example is what is regarded as the earliest book printed in the Philippines, the Doctrina Christiana. Baybayin was used well into the 1800s, however.
Jason Lobel's dissertation: http://www.ling.hawaii.edu/graduate/Dissertations/JasonLobelFinal.pdf
Doctrina Christiana plus an introduction: https://www.gutenberg.org/files/16119/16119-h/16119-h.htm
EDIT: For additional info and context on early Philippine writing and printing see: Ferndández Rodríguez, Rebeca. 2013. ‘Early writing and printing in the Philippines’. History and Philosophy of the Language Sciences. https://hiphilangsci.net/2013/07/10/early-writing-and-printing-in-the-philippines