ext4 is the linux filesystem; it shouldn't have any limitations on the number of files, so we can probably rule out the filesystem.
In order to rule out an issue with media sync, let's try a manual sync over USB:
1) Run sync on AnkiDroid and then sync on Anki Desktop to get both clients in sync
2) Export your full collection from Anki Desktop including scheduling and media
3) Copy the exported apkg file over to your Android device
4) Import the apkg into AnkiDroid
See
here for a bit more detail if you don't understand any of those steps.
If it's still not working after this then upload the apkg from above to Google Drive and post a link here