It happened to me but on a raspberry, when the sd card got way too much stored games, it causes crash, bug while navigating on the menu.
Fortunately i found the solution after a research (it works for all storage support)
-All formatting programs doesn't erase the partitions on the SD card, or USB card (like SD formatter etc.) except one : Rufus formatter.
Got my SD card for Ps2 full and the same for my raspberry (for games until 32 bits, except saturn) as all storage device got a partition : that program erase it as some problems occurs when an storage is full (but with a partition of course).
https://rufus.ie/en/
I hope it will resolve your problem. Ah yes, about PS2 emulation you should try to download LRPS2 core from retroarch (if it's possible on Series X) : you just have to up the anti aliasing SSAA to *16 and there's a choice to up the resolution but with another way than all others emulator. Something more natural.
It's a brand new emulator (like vibration missing) but already the one providing what should looks like a PS2 HD without any sort of glitches in any games.
Even Ridge Racer 5 (a super hard game to emulate correctly) looks like an HD remake.