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That is pretty weird. Which OS are you using?

64-bit Windows 10, Lenovo ThinkPad E480. I once had a similar glitch in Godot but it only happened in the editor. I remember reading that this game was made in Godot as well.

Dang... I cannot replicate this... I've never seen parts of the tilemap disappearing like that... I would get it if all the thing went away but just parts of it is beyond my understanding. 

https://www.reddit.com/r/godot/comments/9ljor3/psa_tilemap_flickering_possible_f...

This could help, however it seems like it doesn't work always. Having this problem in the editor was very annoying (it hasn't happened after I updated Godot). Anyway, I've enjoyed this game a lot so far!

Thanks but this does not seem to be a flickering issue.