After playing the game for some minutes I took a nap and when I tried to play the game again it didn't let me get into a ship so I tried restarting the game, when I tried it I got some errors and after those errors the game got deleted by itself more than the half of the archives and folders... how can I fix this?

This is the third time this week PSO2 has deleted itself, I have now wasted over 300 GB of OS data which not only goes rouge, but invisible.

Welcome to PSO2 NA! This is a known issue that was... "fixed" in the last update. "IT JUST WORKS!"

Here is a guide to uninstall the hidden files: https://www.reddit.com/r/PSO2/comments/grim8e/troubleshooting_if_your_launcher_does_nothing_or/?utm_medium=android_app&utm_source=share

And here's the Tweaker that does what SEGA/Microsoft can't or won't do, fixes the game. works for most (BUT NOT ALL) people without issues. I also recommend disabling antivirus during install and first launch and adding an exception:

https://www.reddit.com/r/PSO2/comments/gv3pdg/new_tweaker_will_fix_all_your_issues_and_not_have/

EDIT: I didn't realize this thread was created a month ago, but MasterDarkwingz at least this should help you now. Next time you may want to consider creating a new post instead of replying in a dead thread. But what do I know, I usually just lurk.