Really glad you've been enjoying the game so much, thank you!
There are a total of six keys in Final Passage and it sounds like you should have found them all. The one (L, U) was guarded by a mini-boss and the one (R, U) needed you to push the three blocks to make notes appear in the correct order - you can double check that one!
Before the v1.1 update that came out a couple of weeks ago there was unfortunately a bug where it was possible to lose two specific keys from your inventory if you died or restarted the game between picking them up and using them in the locks. Sorry if you have run into this! It's fixed now, but if that was the problem you'll need to fix it in the game's save data:
1) Connect your Playdate to a computer over USB and reboot to data disk (Settings > System > Reboot to Data Disk)
2) Open the Playdate disk in your PC file explorer and navigate to Data > pulp.orangethiefltd.resonanttale. There should be a file called store.json inside.
3) Open that file in a text editor like Notepad, find keys and add one to the total. Save that file, disconnect your Playdate, reload the game and you should be good!
Sorry it's a little fiddly! I was kicking myself when I found the bug, so apologies for it slipping through.
If you're not comfortable editing the store.json file, email me at hello at orangethief dot co dot uk and I can make the fix for you. Thanks for supporting the game!