Fe bugs

Lately as I have played Fe I’ve noticed that even though I have finished the main story (right now I’ve been collecting gems), the game often shows cut scenes that I already have played. An example is when you have to sneak past the Silent Ones and also some of the creatures are waiting for me at the start of each world. But as I get closer they glitches and disappear. 

I play the game on my Nintendo Switch and I really don’t want to reinstall it from E-shop, because I am afraid that I will lose my progress so far.

Any tips to how it can be fixed?