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After two years this bug is still there.

see topic:
viewtopic.php?f=52&t=11788#p109627

Editing colors in the color and texture layer causes a bug.
we are trying to replace all the colors from a C&T layer but after apply changes some squigles wont work anymore....
after editing all colors one no longer works...leaving holes where there first was color. its a bit hard to replicate but with enough frames and enough squigle colors it will happen.

Hi Peter,

Do you still have those issues?
I tested on v11.5.2 on a project with ~10 colors, and I can't replicate it.

it seems to work fine now.